[galaxy-commits] commit/galaxy-central: 24 new changesets

24 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1d0bb560bd3d/ changeset: 1d0bb560bd3d user: ichorny date: 2011-10-21 23:01:48 summary: add actual user changes to galaxy-central affected #: 14 files diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -10,7 +10,7 @@ from galaxy.util.json import from_json_string from galaxy.util.expressions import ExpressionContext from galaxy.jobs.actions.post import ActionBox - +import subprocess, pwd from sqlalchemy.sql.expression import and_, or_ import pkg_resources @@ -362,6 +362,9 @@ self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) + if self.app.config.drmaa_external_runjob_script: + os.chmod(self.working_directory , 0777) + # Restore parameters from the database job = self.get_job() if job.user is None and job.galaxy_session is None: @@ -695,6 +698,16 @@ # fix permissions for path in [ dp.real_path for dp in self.get_output_fnames() ]: + #change the ownership of the files in file_path directory back to galaxy user + if self.app.config.drmaa_external_runjob_script and self.app.config.external_chown_script: + galaxy_user_name = pwd.getpwuid(os.getuid())[0] + galaxy_group_id = str(pwd.getpwuid(os.getuid())[3]) + p = subprocess.Popen([ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, path,galaxy_user_name,galaxy_group_id], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + (stdoutdata, stderrdata) = p.communicate() + exitcode = p.returncode + if exitcode != 0: + ## There was an error in the child process + raise RuntimeError("External_chown_script failed (exit code %s) with error %s" % (str(exitcode), stderrdata)) util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) @@ -765,7 +778,7 @@ jeha_false_path = None if self.app.config.outputs_to_working_directory: self.output_paths = [] - self.output_dataset_paths = {} + output_dataset_paths = {} for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) dsp = DatasetPath( data.id, data.file_name, false_path ) @@ -895,7 +908,7 @@ else: self.prepare_input_files_cmds = None self.status = task.states.NEW - + def get_job( self ): if self.job_id: return self.sa_session.query( model.Job ).get( self.job_id ) @@ -1123,7 +1136,7 @@ def __get_runner_name( self, job_wrapper ): if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): - runnner_name = "tasks" + runner_name = "tasks" else: runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0] return runner_name diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -1,4 +1,10 @@ import os, sys, logging, threading, time +import pprint, pwd +from pwd import getpwnam +import subprocess +import inspect +import simplejson as json + from Queue import Queue, Empty from galaxy import model @@ -8,6 +14,7 @@ import pkg_resources + if sys.version_info[:2] == ( 2, 4 ): pkg_resources.require( "ctypes" ) pkg_resources.require( "drmaa" ) @@ -42,9 +49,23 @@ fi export PYTHONPATH fi +%s cd %s %s +%s +%s +%s """ +def __lineno__(): + """Returns the current line number in our program.""" + return inspect.currentframe().f_back.f_lineno + +def __filename__(): + """Returns the current filename in our program.""" + return inspect.currentframe().f_back.f_code.co_filename + +DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification', + 'name','email','project' ] class DRMAAJobState( object ): def __init__( self ): @@ -90,6 +111,10 @@ worker.start() self.work_threads.append( worker ) log.debug( "%d workers ready" % nworkers ) + # external_runJob_script can be None, in which case it's not used. + self.external_runJob_script = app.config.drmaa_external_runjob_script + self.external_killJob_script = app.config.drmaa_external_killjob_script + self.TMPDIR = app.config.TMPDIR def get_native_spec( self, url ): """Get any native DRM arguments specified by the site configuration""" @@ -118,7 +143,6 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - try: job_wrapper.prepare() command_line = self.build_command_line( job_wrapper, include_metadata=True ) @@ -128,7 +152,7 @@ return runner_url = job_wrapper.get_job_runner() - + # This is silly, why would we queue a job with no command line? if not command_line: job_wrapper.finish( '', '' ) @@ -144,8 +168,8 @@ job_wrapper.change_state( model.Job.states.QUEUED ) # define job attributes - ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id) - efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id) + ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) + efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile @@ -153,17 +177,31 @@ native_spec = self.get_native_spec( runner_url ) if native_spec is not None: jt.nativeSpecification = native_spec + #set and export galaxy user PATH enviroment to actual user if submitting jobs as actual user + try: + if self.external_runJob_script: + export_path = 'export PATH=%s:$PATH' %(os.environ['PATH']) + else: + export_path = '' + except: + export_path = '' + + if self.TMPDIR: + export_tmp = 'export TMPDIR=%s' %self.TMPDIR + else: + export_tmp = '' - script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - try: - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) - except: - job_wrapper.fail( "failure preparing job script", exception=True ) - log.exception("failure running job %s" % job_wrapper.get_id_tag()) - return + if self.external_runJob_script == None: + script = drm_template % (job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ),export_tmp, command_line,'','') + else: + touchcmd = 'touch ' + os.path.abspath( job_wrapper.working_directory ) + '/just_in_cases.txt' + chmodcmd = 'chmod -Rf a+rwx ' + os.path.abspath( job_wrapper.working_directory ) + '/*' + script = drm_template % (job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ), export_tmp, command_line, touchcmd,chmodcmd) + + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0755 ) # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: @@ -178,7 +216,12 @@ log.debug("(%s) submitting file %s" % ( galaxy_id_tag, jt.remoteCommand ) ) log.debug("(%s) command is: %s" % ( galaxy_id_tag, command_line ) ) # runJob will raise if there's a submit problem - job_id = self.ds.runJob(jt) + if self.external_runJob_script is None: + job_id = self.ds.runJob(jt) + else: + userid = self.get_qsub_user(job_wrapper) + filename = self.store_jobtemplate(job_wrapper, jt) + job_id = self.external_runjob(filename, userid) log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) ) # store runner information for tracking if Galaxy restarts @@ -272,15 +315,23 @@ efile = drm_job_state.efile job_file = drm_job_state.job_file # collect the output - try: - ofh = file(ofile, "r") - efh = file(efile, "r") - stdout = ofh.read( 32768 ) - stderr = efh.read( 32768 ) - except: - stdout = '' - stderr = 'Job output not returned from cluster' - log.debug(stderr) + # JED - HACK to wait for the files to appear + which_try = 0 + while which_try < 60: + try: + ofh = file(ofile, "r") + efh = file(efile, "r") + stdout = ofh.read( 32768 ) + stderr = efh.read( 32768 ) + which_try = 60 + except: + if which_try == 60: + stdout = '' + stderr = 'Job output not returned from cluster' + log.debug(stderr) + else: + which_try += 1 + time.sleep(1) try: drm_job_state.job_wrapper.finish( stdout, stderr ) @@ -320,13 +371,20 @@ def stop_job( self, job ): """Attempts to delete a job from the DRM queue""" - try: - self.ds.control( job.job_runner_external_id, drmaa.JobControlAction.TERMINATE ) - log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) - except drmaa.InvalidJobException: - log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.id, job.job_runner_external_id ) ) - except Exception, e: - log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) + if self.external_killJob_script is None: + try: + self.ds.control( job.job_runner_external_id, drmaa.JobControlAction.TERMINATE ) + log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) + except drmaa.InvalidJobException: + log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.id, job.job_runner_external_id ) ) + except Exception, e: + log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) + else: + try: + subprocess.Popen(['/usr/bin/sudo','-E', self.external_killJob_script, str(job.job_runner_external_id), str(self.job_user_uid[2])],shell=False) + log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) + except Exception, e: + log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" @@ -348,3 +406,52 @@ drm_job_state.old_state = drmaa.JobState.QUEUED_ACTIVE drm_job_state.running = False self.monitor_queue.put( drm_job_state ) + + def get_qsub_user(self, job_wrapper): + """ Returns the UserID (or Username) that should be used to execute the job. """ + #TODO: + #add some logic to decide on an SGE user for the given job. + job_user_name = job_wrapper.user.split('@') + self.job_user_uid = getpwnam(job_user_name[0]) + log.debug (" (%s) is the uid being passed to the DRM queu\n" % ( self.job_user_uid[2]) ) + return self.job_user_uid[2] + + def store_jobtemplate(self, job_wrapper, jt): + """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string. + Path is hard-coded, but it's no worse than other path in this module. + Uses Galaxy's JobID, so file is expected to be unique.""" + filename = "%s/database/pbs/%s.jt_json" % (os.getcwd(), job_wrapper.get_id_tag()) + data = {} + for attr in DRMAA_jobTemplate_attributes: + try: + data[attr] = getattr(jt, attr) + except: + pass + s = json.dumps(data); + f = open(filename,'w') + f.write(s) + f.close() + return filename + + def external_runjob(self, jobtemplate_filename, username): + """ runs an external script the will QSUB a new job. + The external script will be run with sudo, and will setuid() to the specified user. + Effectively, will QSUB as a different user (then the one used by Galaxy). + """ + p = subprocess.Popen([ '/usr/bin/sudo', '-E', self.external_runJob_script, str(username), jobtemplate_filename ], + shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + (stdoutdata, stderrdata) = p.communicate() + exitcode = p.returncode + #os.unlink(jobtemplate_filename) + if exitcode != 0: + # There was an error in the child process + raise RuntimeError("External_runjob failed (exit code %s)\nCalled from %s:%d\nChild process reported error:\n%s" % (str(exitcode), __filename__(), __lineno__(), stderrdata)) + if not stdoutdata.strip(): + raise RuntimeError("External_runjob did return the job id: %s" % (stdoutdata)) + + # The expected output is a single line containing a single numeric value: + # the DRMAA job-ID. If not the case, will throw an error. + jobId = stdoutdata + return jobId; + + diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -33,6 +33,7 @@ subdir_index[0] = subdir_index[0] + 1 if not os.path.exists(dir): os.makedirs(dir) + os.chmod(dir,0777) task_dirs.append(dir) return dir diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -480,6 +480,23 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + def get_api_value( self, view='collection', value_mapper = None ): + if value_mapper is None: + value_mapper = {} + rval = {} + try: + visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) + except AttributeError: + raise Exception( 'Unknown API view: %s' % view ) + for key in visible_keys: + try: + rval[key] = self.__getattribute__( key ) + if key in value_mapper: + rval[key] = value_mapper.get( key )( rval[key] ) + except AttributeError: + rval[key] = None + return rval + class HistoryUserShareAssociation( object ): def __init__( self ): self.history = None @@ -632,7 +649,7 @@ permitted_actions = get_permitted_actions( filter='DATASET' ) file_path = "/tmp/" engine = None - def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ): + def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True): self.id = id self.state = state self.deleted = False @@ -653,6 +670,7 @@ # Create directory if it does not exist if not os.path.exists( dir ): os.makedirs( dir ) + os.chmod(dir, 0777) # Return filename inside hashed directory return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) else: @@ -1131,6 +1149,28 @@ return hda_name def get_access_roles( self, trans ): return self.dataset.get_access_roles( trans ) + def get_api_value( self, view='collection' ): + # Since this class is a proxy to rather complex attributes we want to + # display in other objects, we can't use the simpler method used by + # other model classes. + hda = self + rval = dict( name = hda.name, + extension = hda.extension, + deleted = hda.deleted, + visible = hda.visible, + state = hda.state, + file_size = int( hda.get_size() ), + genome_build = hda.dbkey, + misc_info = hda.info, + misc_blurb = hda.blurb ) + for name, spec in hda.metadata.spec.items(): + val = hda.metadata.get( name ) + if isinstance( val, MetadataFile ): + val = val.file_name + elif isinstance( val, list ): + val = ', '.join( [str(v) for v in val] ) + rval['metadata_' + name] = val + return rval def quota_amount( self, user ): """ If the user has multiple instances of this dataset, it will not affect their disk usage statistic. @@ -1794,6 +1834,8 @@ # File Exists is okay, otherwise reraise if e.errno != errno.EEXIST: raise + + os.chmod(path, 0777) # Return filename inside hashed directory return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -29,6 +29,9 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify +from galaxy.web import security +import socket + log = logging.getLogger( __name__ ) @@ -104,14 +107,6 @@ try: path = elem.get( "file" ) tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) - if guid is not None: - # Tool was installed from a Galaxy tool shed. - tool.tool_shed = elem.find( "tool_shed" ).text - tool.repository_name = elem.find( "repository_name" ).text - tool.repository_owner = elem.find( "repository_owner" ).text - tool.changeset_revision = elem.find( "changeset_revision" ).text - tool.old_id = elem.find( "id" ).text - tool.version = elem.find( "version" ).text if self.app.config.get_bool( 'enable_tool_tags', False ): tag_names = elem.get( "tags", "" ).split( "," ) for tag_name in tag_names: @@ -372,7 +367,9 @@ # legacy basic mode - provide compatible defaults self.attributes['split_size'] = 20 self.attributes['split_mode'] = 'number_of_parts' - + + + class Tool: """ Represents a computational tool that can be executed through Galaxy. @@ -393,15 +390,9 @@ # easily ensure that parameter dependencies like index files or # tool_data_table_conf.xml entries exist. self.input_params = [] - # Attributes of tools installed from Galaxy tool sheds. - self.tool_shed = None - self.repository_name = None - self.repository_owner = None - self.changeset_revision = None - self.old_id = None - self.version = None # Parse XML element containing configuration self.parse( root, guid=guid ) + self.external_runJob_script = app.config.drmaa_external_runjob_script @property def sa_session( self ): @@ -420,14 +411,14 @@ raise Exception, "Missing tool 'name'" # Get the UNIQUE id for the tool # TODO: can this be generated automatically? - if guid is None: + if guid is not None: + self.id = guid + else: self.id = root.get( "id" ) - self.version = root.get( "version" ) - else: - self.id = guid if not self.id: - raise Exception, "Missing tool 'id'" - if not self.version: + raise Exception, "Missing tool 'id'" + self.version = root.get( "version" ) + if not self.version: # For backward compatibility, some tools may not have versions yet. self.version = "1.0.0" # Support multi-byte tools @@ -814,8 +805,7 @@ if elem.tag == "repeat": group = Repeat() group.name = elem.get( "name" ) - group.title = elem.get( "title" ) - group.help = elem.get( "help", None ) + group.title = elem.get( "title" ) group.inputs = self.parse_input_elem( elem, enctypes, context ) group.default = int( elem.get( "default", 0 ) ) group.min = int( elem.get( "min", 0 ) ) @@ -1578,13 +1568,13 @@ DatasetFilenameWrapper( converted_dataset, datatypes_registry = self.app.datatypes_registry, tool = Bunch( conversion_name = Bunch( extensions = conv_ext ) ), - name = conversion_name ) + name = conversion_name, config_info = self.app.config ) # Wrap actual input dataset input_values[ input.name ] = \ - DatasetFilenameWrapper( input_values[ input.name ], + DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, tool = self, - name = input.name ) + name = input.name, config_info = self.app.config ) elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app, other_values = param_dict ) @@ -1622,28 +1612,28 @@ param_dict[name] = DatasetFilenameWrapper( data, datatypes_registry = self.app.datatypes_registry, tool = self, - name = name ) + name = name, config_info = self.app.config ) if data: for child in data.children: - param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) + param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child,config_info = self.app.config ) for name, hda in output_datasets.items(): # Write outputs to the working directory (for security purposes) # if desired. if self.app.config.outputs_to_working_directory: try: false_path = [ dp.false_path for dp in output_paths if dp.real_path == hda.file_name ][0] - param_dict[name] = DatasetFilenameWrapper( hda, false_path = false_path ) + param_dict[name] = DatasetFilenameWrapper( hda, false_path = false_path, config_info = self.app.config ) open( false_path, 'w' ).close() except IndexError: log.warning( "Unable to determine alternate path for writing job outputs, outputs will be written to their real paths" ) - param_dict[name] = DatasetFilenameWrapper( hda ) + param_dict[name] = DatasetFilenameWrapper( hda, config_info = self.app.config ) else: - param_dict[name] = DatasetFilenameWrapper( hda ) + param_dict[name] = DatasetFilenameWrapper( hda, config_info = self.app.config ) # Provide access to a path to store additional files # TODO: path munging for cluster/dataset server relocatability param_dict[name].files_path = os.path.abspath(os.path.join( job_working_directory, "dataset_%s_files" % (hda.dataset.id) )) for child in hda.children: - param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) + param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child, config_info = self.app.config ) for out_name, output in self.outputs.iteritems(): if out_name not in param_dict and output.filters: # Assume the reason we lack this output is because a filter @@ -1702,8 +1692,10 @@ fd, config_filename = tempfile.mkstemp( dir=directory ) os.close( fd ) f = open( config_filename, "wt" ) + os.chmod(config_filename, 0777) f.write( fill_template( template_text, context=param_dict ) ) f.close() + os.chmod(config_filename, 0777) param_dict[name] = config_filename config_filenames.append( config_filename ) return config_filenames @@ -1836,13 +1828,15 @@ """ for name, hda in output.items(): temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) - try: - if len( os.listdir( temp_file_path ) ) > 0: - store_file_path = os.path.join( - os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), + #try: + if os.path.exists(temp_file_path) and len( os.listdir( temp_file_path ) ) > 0: + store_file_path = os.path.join( + os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), "dataset_%d_files" % hda.dataset.id ) - shutil.move( temp_file_path, store_file_path ) - # Fix permissions + os.mkdir(store_file_path) + os.system('mv %s/* %s/' %(temp_file_path ,store_file_path)) + # Fix permissions + if self.external_runJob_script == None: for basedir, dirs, files in os.walk( store_file_path ): util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid ) for file in files: @@ -1851,8 +1845,8 @@ if os.path.islink( path ): continue util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) - except: - continue + #except: + #continue def collect_child_datasets( self, output): """ @@ -2243,7 +2237,7 @@ def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) - def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None ): + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None , config_info=None): if not dataset: try: # TODO: allow this to work when working with grouping @@ -2255,6 +2249,14 @@ self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) self.false_path = false_path + + # create web_display_url attribute + sec = security.SecurityHelper( id_secret=config_info.id_secret ) + try: + url = 'http://' + socket.getfqdn() + config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) + '/display/?preview=True' + self.web_display_url = url + except: + self.web_display_url = None def __str__( self ): if self.false_path is not None: diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -150,7 +150,7 @@ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = trans.app.datatypes_registry, tool = tool, - name = input.name ) + name = input.name, config_info = trans.app.config) elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) else: @@ -282,9 +282,12 @@ trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) # Create an empty file immediately - open( data.file_name, "w" ).close() - # Fix permissions - util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 ) + self.external_runJob_script = trans.app.config.drmaa_external_runjob_script + if self.external_runJob_script == None: + open( data.file_name, "w" ).close() + # Fix permissions + util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666) + log.debug('.DAT file name = %s\n' %(data.file_name)) # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -279,8 +279,10 @@ is_binary = None try: link_data_only = uploaded_dataset.link_data_only + chmod_flag = 1 except: link_data_only = 'copy_files' + chmod_flag = 0 json = dict( file_type = uploaded_dataset.file_type, ext = uploaded_dataset.ext, name = uploaded_dataset.name, @@ -291,8 +293,12 @@ link_data_only = link_data_only, space_to_tab = uploaded_dataset.space_to_tab, path = uploaded_dataset.path ) + if chmod_flag == 0 and trans.app.config.drmaa_external_runjob_script: + os.chmod(uploaded_dataset.path, 0777) json_file.write( to_json_string( json ) + '\n' ) json_file.close() + if trans.app.config.drmaa_external_runjob_script: + os.chmod(json_file_path, 0777) return json_file_path def create_job( trans, params, tool, json_file_path, data_list, folder=None, return_job=False ): """ @@ -325,12 +331,17 @@ # Create an empty file immediately if not dataset.dataset.external_filename: open( dataset.file_name, "w" ).close() + if trans.app.config.drmaa_external_runjob_script: + os.chmod(dataset.file_name, 0777) else: for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) # Create an empty file immediately if not dataset.dataset.external_filename: open( dataset.file_name, "w" ).close() + if trans.app.config.drmaa_external_runjob_script: + os.chmod(dataset.file_name, 0777) + job.state = job.states.NEW trans.sa_session.add( job ) trans.sa_session.flush() diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 scripts/drmaa_external_killer.py --- /dev/null +++ b/scripts/drmaa_external_killer.py @@ -0,0 +1,63 @@ +#!/usr/bin/env python +import os +import sys +import errno +import pwd +#import drmaa +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require("simplejson") +import simplejson as json +pkg_resources.require("drmaa") +import drmaa + + + +def validate_paramters(): + if len(sys.argv)<3: + sys.stderr.write("usage: %s [job ID] [user uid]\n" % sys.argv[0]) + exit(1) + + jobID = sys.argv[1] + uid = int(sys.argv[2]) + + + + return jobID, uid + +def set_user(uid): + try: + gid = pwd.getpwuid(uid).pw_gid + os.setgid(gid) + os.setuid(uid) + except OSError, e: + if e.errno == errno.EPERM: + sys.stderr.write("error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid ) + exit(1) + else: + pass + if os.getuid()==0: + sys.stderr.write("error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n" ) + exit(1) + if os.geteuid()==0: + sys.stderr.write("error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n" ) + exit(1) + +def main(): + jobID, uid = validate_paramters() + set_user(uid) + s=drmaa.Session() + s.initialize() + s.control(jobID,drmaa.JobControlAction.TERMINATE) + s.exit() + + + +if __name__ == "__main__": + main() + + diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 scripts/drmaa_external_runner.py --- /dev/null +++ b/scripts/drmaa_external_runner.py @@ -0,0 +1,108 @@ +#!/usr/bin/env python +import os +import sys +import errno +import pwd + +#import simplejson as json +#import drmaa +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require("simplejson") +import simplejson as json +pkg_resources.require("drmaa") +import drmaa + +DRMAA_jobTemplate_attributes = [ 'args', 'remoteCommand', 'outputPath', 'errorPath', 'nativeSpecification', + 'name','email','project' ] + +def load_job_template_from_file(jt, filename): + f = open(filename,'r') + data = json.load(f) + for attr in DRMAA_jobTemplate_attributes: + if attr in data: + setattr(jt, attr, data[attr]) + +def valid_numeric_userid(userid): + try: + uid = int(userid) + except: + return False + try: + pw = pwd.getpwuid(uid) + except KeyError: + sys.stderr.write("error: User-ID (%d) is not valid.\n" % uid) + exit(1) + return True + +def get_user_id_by_name(username): + try: + pw = pwd.getpwnam(username) + except KeyError: + sys.stderr.write("error: User name (%s) is not valid.\n" % username) + exit(1) + return pw.pw_uid +def validate_paramters(): + if len(sys.argv)<3: + sys.stderr.write("usage: %s [USER-ID] [JSON-JOB-TEMPLATE-FILE]\n" % sys.argv[0]) + exit(1) + + userid = sys.argv[1] + json_filename = sys.argv[2] + + if valid_numeric_userid(userid): + uid = int(userid) + else: + uid = get_user_id_by_name(userid) + + if uid == 0: + sys.stderr.write("error: userid must not be 0 (root)\n") + exit(1) + + if not os.path.exists(json_filename): + sys.stderr.write("error: JobTemplate file (%s) doesn't exist\n" % ( json_filename ) ) + exit(1) + + return uid, json_filename + +def set_user(uid): + try: + # Get user's default group and set it to current process to make sure file permissions are inherited correctly + # Solves issue with permission denied for JSON files + gid = pwd.getpwuid(uid).pw_gid + os.setgid(gid) + os.setuid(uid) + except OSError, e: + if e.errno == errno.EPERM: + sys.stderr.write("error: setuid(%d) failed: permission denied. Did you setup 'sudo' correctly for this script?\n" % uid ) + exit(1) + else: + pass + if os.getuid()==0: + sys.stderr.write("error: UID is 0 (root) after changing user. This script should not be run as root. aborting.\n" ) + exit(1) + if os.geteuid()==0: + sys.stderr.write("error: EUID is 0 (root) after changing user. This script should not be run as root. aborting.\n" ) + exit(1) +def main(): + userid, json_filename = validate_paramters() + set_user(userid) + s = drmaa.Session() + s.initialize() + jt = s.createJobTemplate() + load_job_template_from_file(jt, json_filename) + # runJob will raise if there's a submittion error + jobId = s.runJob(jt) + s.deleteJobTemplate(jt) + s.exit() + + # Print the Job-ID and exit. Galaxy will pick it up from there. + print jobId + +if __name__ == "__main__": + main() + diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 scripts/external_chown_script.py --- /dev/null +++ b/scripts/external_chown_script.py @@ -0,0 +1,43 @@ +#!/usr/bin/env python +import os +import sys +import errno +import pwd +#import drmaa +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require("simplejson") +import simplejson as json +pkg_resources.require("drmaa") +import drmaa + + + +def validate_paramters(): + if len(sys.argv)<4: + sys.stderr.write("usage: %s path user_name gid\n" % sys.argv[0]) + exit(1) + + path = sys.argv[1] + galaxy_user_name = sys.argv[2] + gid = sys.argv[3] + + + + return path, galaxy_user_name, gid + +def main(): + path, galaxy_user_name, gid = validate_paramters() + os.system('chown %s %s' %(galaxy_user_name, path)) + os.system('chgrp %s %s' %(gid, path)) + + + +if __name__ == "__main__": + main() + + diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -165,6 +165,7 @@ dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) dataset.name = dataset.name.rstrip( '.gz' ) data_type = 'gzip' if not data_type and bz2 is not None: @@ -197,6 +198,7 @@ dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) dataset.name = dataset.name.rstrip( '.bz2' ) data_type = 'bz2' if not data_type: @@ -253,6 +255,7 @@ dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) + os.chmod(dataset.path, 0644) dataset.name = uncompressed_name data_type = 'zip' if not data_type: @@ -312,9 +315,18 @@ pass else: # This should not happen, but it's here just in case - shutil.copy( dataset.path, output_path ) + shutil.move( dataset.path, output_path ) + try: + os.chmod(output_path,0644) + except: + pass elif link_data_only == 'copy_files': shutil.move( dataset.path, output_path ) + try: + os.chmod(output_path,0644) + except: + pass + # Write the job info stdout = stdout or 'uploaded %s file' % data_type info = dict( type = 'dataset', diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,5 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.5"> - <!-- Wrapper supports Cufflinks versions v1.0.0-v1.0.3 --> +<tool id="cufflinks" name="Cufflinks" version="0.9.1"><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> @@ -15,10 +14,27 @@ ## Include reference annotation? #if $reference_annotation.use_ref == "Use reference annotation": - -G $reference_annotation.reference_annotation_file + #if $reference_annotation.annotationSource.reference_annotation_file == "indexed": + -G "${ filter( lambda x: str( x[0] ) == str( $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + #if $reference_annotation.annotationSource.reference_annotation_file == "attribute": + -G "${ filter( lambda x: str( x[0] ) == str( $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + -G "${reference_annotation.annotationSource.ownFile}" + #end if + #end if #end if + #if $reference_annotation.use_ref == "Use reference annotation guide": - -g $reference_annotation.reference_annotation_guide_file + #if $reference_annotation.annotationSource.reference_annotation_file == "indexed": + -g "${ filter( lambda x: str( x[0] ) == str( $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + #if $reference_annotation.annotationSource.reference_annotation_file == "attribute": + -g "${ filter( lambda x: str( x[0] ) == str( $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + -g "${reference_annotation.annotationSource.ownFile}" + #end if + #end if #end if ## Set paired-end parameters? @@ -61,10 +77,44 @@ </param><when value="No"></when><when value="Use reference annotation"> - <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> - </when> + <conditional name="annotationSource"> + <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + <option value="attribute">Use input bam metadata.dbkey attribute</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select genome for gtf annotation"> + <options from_data_table="gtf_index"> + <filter type="sort_by" column="3" /> + <validator type="no_options" message="No indexes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> + </when> + </conditional> + </when><when value="Use reference annotation guide"> - <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <conditional name="annotationSource"> + <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + <option value="attribute">Use input bam metadata.dbkey attribute</option> + </param> + <when value="indexed"> + <param name="indices" type="select" label="Select genome for gtf annotation"> + <options from_data_table="gtf_index"> + <filter type="sort_by" column="3" /> + <validator type="no_options" message="No indexes are available for the selected input dataset" /> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> + </when> + </conditional></when></conditional><conditional name="bias_correction"> diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,7 +1,8 @@ -<tool id="tophat" name="Tophat for Illumina" version="1.5.0"> +<tool id="tophat" name="Tophat" version="1.2.1"><description>Find splice junctions using RNA-seq data</description> - <version_command>tophat --version</version_command><requirements> + <requirement type="package">samtools</requirement> + <requirement type="package">bowtie</requirement><requirement type="package">tophat</requirement></requirements><command interpreter="python"> @@ -17,14 +18,18 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + #if $refGenomeSource.genomeSource == "indexed": + --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + #else: + --indexes-path="${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + #end if #end if ## Are reads single-end or paired? --single-paired=$singlePaired.sPaired ## First input file always required. - --input1=$input1 + --input1=$singlePaired.input1 ## Set params based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": @@ -52,7 +57,15 @@ ## Supplying junctions parameters. #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes": - -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model + #if $singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "indexed": + -G "${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + #if $singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "attribute": + -G "${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else + -G "${singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.owngtfFile}" + #end if + #end if #end if #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes": -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs @@ -111,7 +124,15 @@ ## Supplying junctions parameters. #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes": - -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model + #if $singlePaired.pParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "indexed": + -G "${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else: + #if $singlePaired.pParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "attribute": + -G "${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" + #else + -G "${singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.owngtfFile}" + #end if + #end if #end if #if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes": -j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs @@ -145,18 +166,15 @@ #end if </command><inputs> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option><option value="history">Use one from the history</option> + <option value="attribute">Use input fastq metadata.dbkey attribute</option></param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="tophat_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> + <options from_data_table="tophat_indexes" /></param></when><when value="history"> @@ -169,6 +187,7 @@ <option value="paired">Paired-end</option></param><when value="single"> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><conditional name="sParams"><param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."><option value="preSet">Use Defaults</option> @@ -218,7 +237,16 @@ </param><when value="No" /><when value="Yes"> - <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + <conditional name="annotationSource"> + <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + <option value="attribute">Use metadata.bkey attribute from input fastq file</option> + </param> + <when value="history"> + <param name="owngtfFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> + </when> + </conditional></when></conditional><conditional name="raw_juncs"> @@ -263,7 +291,7 @@ <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /></when><when value="No" /> - </conditional> + </conditional><param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option> @@ -272,7 +300,8 @@ </conditional><!-- sParams --></when><!-- single --><when value="paired"> - <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /><conditional name="pParams"><param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> @@ -323,7 +352,16 @@ </param><when value="No" /><when value="Yes"> - <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + <conditional name="annotationSource"> + <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + <option value="attribute">Use metadata.bkey attribute from input fastq files</option> + </param> + <when value="history"> + <param name="owngtfFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> + </when> + </conditional></when></conditional><conditional name="raw_juncs"> @@ -387,7 +425,7 @@ ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) - ) + ) </filter><actions><conditional name="refGenomeSource.genomeSource"> @@ -475,49 +513,46 @@ </outputs><tests> - <!-- Test base-space single-end reads with pre-built index and preset parameters --> + <!-- Test single-end reads with pre-built index and preset parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger - Rename the files in tmp_dir appropriately + tophat -o tmp_dir -p 1 /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger --> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="genomeSource" value="indexed" /><param name="index" value="tophat_test" /><param name="sPaired" value="single" /> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /><output name="junctions" file="tophat_out1j.bed" /><output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test> - <!-- Test using base-space test data: paired-end reads, index from history. --> + <!-- Test using test data: paired-end reads, index from history. --><test><!-- TopHat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger - Rename the files in tmp_dir appropriately --> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="genomeSource" value="history" /><param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /><param name="sPaired" value="paired" /> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="mate_inner_distance" value="20" /><param name="pSettingsType" value="preSet" /><output name="junctions" file="tophat_out2j.bed" /><output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test> - <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters --> + <!-- Test single-end reads with user-supplied reference fasta and full parameters --><test><!-- Tophat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger Replace the + with double-dash - Rename the files in tmp_dir appropriately --> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="genomeSource" value="history"/><param name="ownFile" value="tophat_in1.fasta"/><param name="sPaired" value="single"/> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="sSettingsType" value="full"/><param name="library_type" value="FR Unstranded"/><param name="anchor_length" value="8"/> @@ -550,17 +585,16 @@ <output name="junctions" file="tophat_out3j.bed" /><output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" /></test> - <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters --> + <!-- Test paired-end reads with user-supplied reference fasta and full parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger + tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger Replace the + with double-dash - Rename the files in tmp_dir appropriately --> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="genomeSource" value="indexed"/><param name="index" value="tophat_test"/><param name="sPaired" value="paired"/> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="full"/> @@ -628,9 +662,7 @@ .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 .. _BAM: http://samtools.sourceforge.net/ - -Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format. - + ------- **Tophat settings** @@ -649,7 +681,7 @@ --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one - read with this many bases on each side. This must be at least 3 and the default is 8. + read with this many bases on each side. This must be at least 3 and the default is 8. -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. diff -r 070513d25b63110ef6569a9b09101864009f2ba4 -r 1d0bb560bd3d584708972001afd054774e9e89c5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -446,6 +446,14 @@ # large servers. #enable_tool_tags = False +# Enable a feature when running workflows. When enabled, default datasets +# are selected for "Set at Runtime" inputs from the history such that the +# same input will not be selected twice, unless there are more inputs than +# compatible datasets in the history. +# When False, the most recently added compatible item in the history will +# be used for each "Set at Runtime" input, independent of others in the Workflow +#enable_unique_workflow_defaults = False + # Enable Galaxy's "Upload via FTP" interface. You'll need to install and # configure an FTP server (we've used ProFTPd since it can use Galaxy's # database for authentication) and set the following two options. @@ -533,6 +541,30 @@ # currently available are 'pbs' and 'drmaa'. #start_job_runners = None +# Uncomment drmaa_external_runjob_script , drmaa_external_killjob_script, and external_chown_script pameters and have them point to the +# absolute path for scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py. +# The scripts directory is located in the top level galaxy directory. The parameters when +# uncommented allow for submission to the drmaa queue with the user name of the user submitting +# the job and not the galaxy user. In order for this to work the actual user must log into galaxy +# and the galaxy authentication must be consistent with the authentication on the server in which the +# drmaa queue is running (i.e. the username must have an account on the server and be allowed to +# submit jobs to the queue). The galaxy user must also be given sudo permission to execute +# scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py in /etc/sudoers +# Example: +# galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_runner.py +# galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_killer.py +# Also the +# Defaults requiretty +# in /etc/sudoers must be commented out +#drmaa_external_runjob_script = /opt/galaxy/scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = /opt/galaxy/scripts/drmaa_external_killer.py +#external_chown_script = /opt/galaxy/scripts/external_chown_script.py + +#important if running as actual user since enviromental variables are not passed +#will supercede an other definition of TMPDIR if using drmaa +#TMPDIR = /opt/galaxy/database/tmp + + # The URL for the default runner to use when a tool doesn't explicitly define a # runner below. #default_cluster_job_runner = local:/// @@ -554,7 +586,9 @@ # run with the runner defined with default_cluster_job_runner. [galaxy:tool_runners] - +binsort = drmaa://-cwd -V -pe threaded 4/ +bwa_wrapper = drmaa://-cwd -V -pe threaded 4/ +unified_genotyper = drmaa://-cwd -V -pe threaded 2/ biomart = local:/// encode_db1 = local:/// hbvar = local:/// https://bitbucket.org/galaxy/galaxy-central/changeset/28ab7dde0972/ changeset: 28ab7dde0972 user: ichorny date: 2011-10-21 23:05:06 summary: merge with galaxy central affected #: 27 files diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -133,6 +133,8 @@ def restore_text(text): """Restores sanitized text""" + if not text: + return text for key, value in mapped_chars.items(): text = text.replace(value, key) return text diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/web/api/histories.py --- a/lib/galaxy/web/api/histories.py +++ b/lib/galaxy/web/api/histories.py @@ -88,9 +88,9 @@ state = states.QUEUED elif summary[states.OK] == num_sets: state = states.OK + item['state_details'] = summary item['contents_url'] = url_for( 'history_contents', history_id=history_id ) item['state'] = state - item['state_details'] = summary except Exception, e: item = "Error in history API at showing history detail" log.error(item + ": %s" % str(e)) diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -14,7 +14,7 @@ log = logging.getLogger( __name__ ) -class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory ): +class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociation, UsesHistory, UsesLibrary, UsesLibraryItems ): @web.expose_api def index( self, trans, history_id, **kwd ): @@ -85,7 +85,7 @@ if from_ld_id: try: - ld = get_library_content_for_access( trans, from_ld_id ) + ld = self.get_library_dataset( trans, from_ld_id, check_ownership=False, check_accessible=False ) assert type( ld ) is trans.app.model.LibraryDataset, "Library content id ( %s ) is not a dataset" % from_ld_id except AssertionError, e: trans.response.status = 400 diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/web/api/library_contents.py --- a/lib/galaxy/web/api/library_contents.py +++ b/lib/galaxy/web/api/library_contents.py @@ -75,9 +75,9 @@ """ class_name, content_id = self.__decode_library_content_id( trans, id ) if class_name == 'LibraryFolder': - content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessibility=True ) + content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True ) else: - content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessibility=True ) + content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True ) return self.encode_all_ids( trans, content.get_api_value( view='element' ) ) @web.expose_api @@ -100,9 +100,10 @@ return "Missing requred 'folder_id' parameter." else: folder_id = payload.pop( 'folder_id' ) + class_name, folder_id = self.__decode_library_content_id( trans, folder_id ) try: # security is checked in the downstream controller - parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessibility=False ) + parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessible=False ) except Exception, e: return str( e ) # The rest of the security happens in the library_common controller. @@ -128,6 +129,23 @@ url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) return rval + @web.expose_api + def update( self, trans, id, library_id, payload, **kwd ): + """ + PUT /api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id} + Sets relationships among items + """ + if 'converted_dataset_id' in payload: + converted_id = payload.pop( 'converted_dataset_id' ) + content = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=False ) + content_conv = self.get_library_dataset( trans, converted_id, check_ownership=False, check_accessible=False ) + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = content.library_dataset_dataset_association, + dataset = content_conv.library_dataset_dataset_association, + file_type = content_conv.library_dataset_dataset_association.extension, + metadata_safe = True ) + trans.sa_session.add( assoc ) + trans.sa_session.flush() + def __decode_library_content_id( self, trans, content_id ): if ( len( content_id ) % 16 == 0 ): return 'LibraryDataset', content_id diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -708,7 +708,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.expose @web.require_admin diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -183,7 +183,7 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) -class DownloadableRepositoryListGrid( RepositoryListGrid ): +class ValidRepositoryListGrid( RepositoryListGrid ): class RevisionColumn( grids.GridColumn ): def __init__( self, col_name ): grids.GridColumn.__init__( self, col_name ) @@ -196,7 +196,7 @@ if len( select_field.options ) > 1: return select_field.get_html() return repository.revision - title = "Downloadable repositories" + title = "Valid repositories" columns = [ RepositoryListGrid.NameColumn( "Name", key="name", @@ -210,11 +210,6 @@ attach_popup=False, key="User.username" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) operations = [] def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) \ @@ -237,7 +232,7 @@ return repository_metadata.repository.user.username return 'no user' # Grid definition - title = "Matched repositories" + title = "Repositories with matching tools" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' default_sort_key = "Repository.name" @@ -282,21 +277,19 @@ .filter( self.model_class.table.c.repository_id == 0 ) class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): - # Grid definition - title = "Repositories that contain tools matching search criteria" columns = [ col for col in MatchedRepositoryListGrid.columns ] # Override the NameColumn columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="galaxy" ) ), - attach_popup=True ) + attach_popup=False ) class RepositoryController( BaseUIController, ItemRatings ): install_matched_repository_list_grid = InstallMatchedRepositoryListGrid() matched_repository_list_grid = MatchedRepositoryListGrid() - downloadable_repository_list_grid = DownloadableRepositoryListGrid() + valid_repository_list_grid = ValidRepositoryListGrid() repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() @@ -340,7 +333,7 @@ # Render the list view return self.category_list_grid( trans, **kwd ) @web.expose - def browse_downloadable_repositories( self, trans, **kwd ): + def browse_valid_repositories( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: @@ -352,6 +345,7 @@ repository = get_repository( trans, repository_id ) return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', + webapp=webapp, repository_id=repository_id, changeset_revision=repository.tip ) ) # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change @@ -371,16 +365,16 @@ webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) - url_args = dict( action='browse_downloadable_repositories', + url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', webapp=webapp, repository_id=repository_id ) - self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", - url_args=url_args, - allow_multiple=False, - async_compatible=False ) ] + self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", + url_args=url_args, + allow_multiple=False, + async_compatible=False ) ] # Render the list view - return self.downloadable_repository_list_grid( trans, **kwd ) + return self.valid_repository_list_grid( trans, **kwd ) @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) @@ -391,38 +385,35 @@ if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) if 'operation' in kwd: - operation = kwd[ 'operation' ].lower() - is_admin = trans.user_is_admin() - if operation == "view_or_manage_repository": - # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) - repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = get_repository( trans, repository_id ) - kwd[ 'id' ] = repository_id - kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): - a = 'manage_repository' - else: - a = 'view_repository' - return trans.response.send_redirect( web.url_for( controller='repository', - action=a, - **kwd ) ) - if operation == "install": - repo_info_dict = {} - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s' % ( galaxy_url, trans.request.host, webapp ) - repository_metadata_ids = util.listify( kwd[ 'id' ] ) - for repository_metadata_id in repository_metadata_ids: - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - repository_id = trans.security.encode_id( repository.id ) - changeset_revision = repository_metadata.changeset_revision - repository_clone_url = generate_clone_url( trans, repository_id ) - repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self.__encode( repo_info_dict ) - url += '&repo_info_dict=%s' % encoded_repo_info_dict - return trans.response.send_redirect( url ) + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) + if operation == "install": + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + # TODO: support https in the following url. + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + return trans.response.send_redirect( url ) + else: + # This can only occur when there is a multi-select grid with check boxes and an operation, + # and the user clicked the operation button without checking any of the check boxes. + return trans.show_error_message( "No items were selected." ) tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] @@ -436,7 +427,12 @@ kwd[ 'match_tuples' ] = match_tuples # Render the list view if webapp == 'galaxy': - # Our request originated from a Galaxy instance. + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations @@ -583,8 +579,21 @@ if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples - def __encode( self, repo_info_dict ): - value = simplejson.dumps( repo_info_dict ) + def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): + repo_info_dict = {} + for repository_metadata_id in repository_metadata_ids: + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_id = trans.security.encode_id( repository.id ) + changeset_revision = repository_metadata.changeset_revision + repository_clone_url = generate_clone_url( trans, repository_id ) + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + return self.__encode( repo_info_dict ) + def __encode( self, val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) b = binascii.hexlify( value ) return "%s:%s" % ( a, b ) @@ -620,14 +629,18 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + repo_info_dict = {} + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + encoded_repo_info_dict = self.__encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. - repository_clone_url = generate_clone_url( trans, repository_id ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, trans.request.host, repository.name, repository.description, repository_clone_url, changeset_revision ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, encoded_repo_info_dict ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -777,6 +777,7 @@ show_item_checkboxes = True %><form action="${url()}" method="post" onsubmit="return false;"> + <input type="hidden" name="webapp" value="${webapp}"/><table id="grid-table" class="grid"><thead id="grid-table-header"><tr> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -10,6 +10,13 @@ %><%inherit file="${inherit(context)}"/> +%if webapp == 'galaxy': + <br/><br/> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + </ul> +%endif + %if message: ${render_msg( message, status )} %endif diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -64,7 +64,12 @@ <br/><br/><ul class="manage-table-actions"> - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div></ul> %if message: diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -111,7 +111,12 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %else: %if is_new: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -94,7 +94,12 @@ </div> %endif %else: - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %endif </ul> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -34,7 +34,12 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </div> %else: %if is_new: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 templates/webapps/galaxy/admin/tool_sheds.mako --- a/templates/webapps/galaxy/admin/tool_sheds.mako +++ b/templates/webapps/galaxy/admin/tool_sheds.mako @@ -16,7 +16,7 @@ <div class="toolFormTitle">Accessible Galaxy tool sheds</div><div class="toolFormBody"><div class="form-row"> - <table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"> + <table class="grid"><% shed_id = 0 %> %for name, url in trans.app.tool_shed_registry.tool_sheds.items(): <tr class="libraryTitle"> @@ -25,7 +25,7 @@ <a class="view-info" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">${name}</a></div><div popupmenu="dataset-${shed_id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse downloadable repositories</a> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a></div></td> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/filters/sff_extract.py --- a/tools/filters/sff_extract.py +++ b/tools/filters/sff_extract.py @@ -27,7 +27,7 @@ __author__ = 'Jose Blanca and Bastien Chevreux' __copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux' __license__ = 'GPLv3 or later' -__version__ = '0.2.8' +__version__ = '0.2.10' __email__ = 'jblanca@btc.upv.es' __status__ = 'beta' @@ -298,7 +298,8 @@ #we check that we're removing the asked tag if tag is not None and tag != last_tag: - raise RuntimeError("The given xml tag wasn't the last one in the file") + etxt=join('The given xml tag (',tag,') was not the last one in the file'); + raise RuntimeError(etxt) # while we are at it: also remove all white spaces in that line :-) i -= 1 @@ -843,7 +844,7 @@ if len(boundaries) == 3: # case: mask char on both sides of sequence #print "bounds3" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] data['clip_adapter_right']=boundaries[2][0] elif len(boundaries) == 2: # case: mask char left or right of sequence @@ -851,7 +852,7 @@ if maskedseq[0] == maskchar : # case: mask char left #print "left" - data['clip_adapter_left']=1+boundaries[0][1] + data['clip_adapter_left']=boundaries[0][1] else: # case: mask char right #print "right" @@ -1192,7 +1193,11 @@ ''' left, right = return_merged_clips(data) seq = data['bases'] - new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + if left >= right: + new_seq = seq.lower() + else: + new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower())) + return new_seq def clip_read(data): @@ -1209,14 +1214,14 @@ -def tests_for_ssaha(linker_fname): +def tests_for_ssaha(): '''Tests whether SSAHA2 can be successfully called.''' try: print "Testing whether SSAHA2 is installed and can be launched ... ", sys.stdout.flush() fh = open('/dev/null', 'w') - retcode = subprocess.call(["ssaha2", "-v"], stdout = fh) + retcode = subprocess.call(["ssaha2"], stdout = fh) fh.close() print "ok." except : @@ -1247,6 +1252,8 @@ '''Launches SSAHA2 on the linker and query file, string SSAHA2 output into the output filehandle''' + tests_for_ssaha() + try: print "Searching linker sequences with SSAHA2 (this may take a while) ... ", sys.stdout.flush() diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/filters/sff_extractor.xml --- a/tools/filters/sff_extractor.xml +++ b/tools/filters/sff_extractor.xml @@ -1,4 +1,4 @@ -<tool id="Sff_extractor" name="SFF converter" version="1.0.0"> +<tool id="Sff_extractor" name="SFF converter" version="1.0.1"><description></description><command interpreter="python"> #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -59,14 +59,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -78,11 +80,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -202,7 +211,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -218,12 +227,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -240,7 +255,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -254,7 +269,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -267,19 +282,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -165,7 +165,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -181,12 +181,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -203,7 +209,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,7 +223,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -230,19 +236,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -47,12 +47,13 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' @@ -67,11 +68,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -151,7 +159,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -167,8 +175,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -191,7 +203,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -205,7 +217,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -218,19 +230,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -35,29 +35,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if - #set $rod_binding_names = dict() - #for $rod_binding in $gatk_param_type.rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector - #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' - #if str( $gatk_param_type.input_dbsnp_rod ) != "None": - -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod" - #end if + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +56,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -147,7 +141,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -163,35 +157,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="snps" selected="True">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> - <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" /> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -208,7 +185,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -222,7 +199,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -235,19 +212,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -56,12 +56,13 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' @@ -76,11 +77,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -194,7 +202,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -210,8 +218,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -234,7 +246,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -248,7 +260,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -261,19 +273,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -89,14 +89,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -108,10 +110,16 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" @@ -252,28 +260,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -281,55 +295,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -37,14 +37,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -56,11 +58,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -118,28 +127,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -147,55 +162,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -28,7 +28,6 @@ --rod_priority_list "${ ','.join( $priority_order ) }" ' - ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": #for $sample_metadata in $gatk_param_type.sample_metadata: @@ -44,13 +43,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -62,11 +64,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -138,7 +147,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -154,12 +163,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -176,7 +191,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -203,19 +218,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -56,13 +56,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -74,11 +77,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -195,7 +205,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -211,12 +221,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -233,7 +249,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -247,7 +263,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -260,19 +276,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -50,14 +50,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +71,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -152,7 +161,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -168,12 +177,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -204,7 +219,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,19 +232,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -58,14 +58,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -77,11 +79,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -382,28 +391,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -411,55 +426,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> diff -r 1d0bb560bd3d584708972001afd054774e9e89c5 -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -42,13 +42,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -60,11 +63,18 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if + #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -120,7 +130,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -136,12 +146,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -158,7 +174,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -172,7 +188,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -185,19 +201,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + </when></conditional> https://bitbucket.org/galaxy/galaxy-central/changeset/603924d3abc3/ changeset: 603924d3abc3 user: ichorny date: 2011-10-21 23:18:09 summary: added altered config.py affected #: 1 file diff -r 28ab7dde097298b7565a6238f0bbcade29a73ae9 -r 603924d3abc3057def82337b53178ad48a71b1d1 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -104,6 +104,10 @@ self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" ) self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" ) self.pbs_stage_path = kwargs.get('pbs_stage_path', "" ) + self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None ) + self.drmaa_external_killjob_script = kwargs.get('drmaa_external_killjob_script', None) + self.external_chown_script = kwargs.get('external_chown_script', None) + self.TMPDIR = kwargs.get('TMPDIR', None) self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) @@ -215,12 +219,21 @@ os.makedirs( path ) except Exception, e: raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) + if self.drmaa_external_runjob_script: + os.chmod(self.new_file_path, 0777) + os.chmod(self.job_working_directory, 0777) + os.chmod(self.cluster_files_directory, 0777) + else: + os.chmod(self.new_file_path, 0755) + os.chmod(self.job_working_directory, 0755) + os.chmod(self.cluster_files_directory, 0755) + # Check that required files exist for path in self.tool_configs: if not os.path.isfile(path): raise ConfigurationError("File not found: %s" % path ) if not os.path.isfile( self.datatypes_config ): - raise ConfigurationError("File not found: %s" % path ) + raise ConfigurationError("File not found: %s" % self.datatypes_config ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: https://bitbucket.org/galaxy/galaxy-central/changeset/125d735c689e/ changeset: 125d735c689e user: natefoo date: 2011-10-25 17:14:04 summary: merge affected #: 50 files diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de README.txt --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ HOW TO START ============ -Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run: +Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: % python -V Python 2.4.4 diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -646,7 +646,7 @@ # TODO: unpack and validate bookmarks: def unpack_bookmarks( bookmarks_json ): - return + return bookmarks_json # Unpack and validate view content. view_content = unpack_collection( decoded_payload[ 'view' ] ) diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/images/fugue/application-dock-270-bw.png Binary file static/images/fugue/application-dock-270-bw.png has changed diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/images/fugue/application-dock-270.png Binary file static/images/fugue/application-dock-270.png has changed diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 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603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/images/fugue/ui-slider-050.png Binary file static/images/fugue/ui-slider-050.png has changed diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -3,9 +3,30 @@ .content{font:10px verdana;} .nav-controls{text-align:center;padding:1px 0;} .nav-controls input{margin:0 5px;} +.menu-button{padding: 0px 4px 0px 4px;} #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;} +.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} +.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} +.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} +.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} +.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} +.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} +.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} +.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} +.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} +.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} +#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} +#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;} +#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} +#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} +#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} +#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;} +#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;} +#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0 10px;} .draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} @@ -19,12 +40,13 @@ .viewport-canvas{width:100%;height:100px;} .yaxislabel{color:#777;z-index:100;} .line-track .track-content{border-top:1px solid #eee;border-bottom:1px solid #eee;} -.group-handle{cursor:move;float:left;background:#eee url('/static/images/tracks/block.png');width:12px;height:12px;} +.group-handle{cursor:move;float:left;background:#eee url('../images/tracks/block.png');width:12px;height:12px;} .group{min-height:20px;border-top:2px solid #888;border-bottom:2px solid #888;} .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;} +.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;} +.track-name{float:left;margin-top:2px;height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -130,7 +130,7 @@ .group-handle { cursor: move; float: left; - background: #eee url('/static/images/tracks/block.png'); + background: #eee url('../images/tracks/block.png'); width: 12px; height: 12px; } @@ -159,10 +159,16 @@ text-align: center; border-top: 1px solid #eee; border-bottom: 2px solid #eee; - background: #eee url('/static/images/tracks/diag_bg.gif'); + background: #eee url('../images/tracks/diag_bg.gif'); min-height: 16px; } +.track-name { + float: left; + margin-top: 2px; + height: 16px; +} + .label-track .track-content { background: white; } @@ -288,6 +294,70 @@ font-weight: bold; padding-top: 0.2em; } +.menu-button { + padding: 0px 4px 0px 4px; +} +.settings-icon { + background: transparent url(../images/fugue/gear-bw.png) no-repeat; +} +.settings-icon:hover { + background: transparent url(../images/fugue/gear.png) no-repeat; +} +.overview-icon { + background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat; +} +.overview-icon:hover { + background:transparent url(../images/fugue/application-dock-270.png) no-repeat; +} + +.tools-icon { + background: transparent url(../images/fugue/toolbox-bw.png) no-repeat; +} +.tools-icon:hover { + background: transparent url(../images/fugue/toolbox.png) no-repeat; +} +.filters-icon { + background: transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat; +} +.filters-icon:hover { + background: transparent url(../images/fugue/ui-slider-050.png) no-repeat; +} +.remove-icon, .overview-close { + background: transparent url(../images/fugue/cross-small-bw.png) no-repeat; +} +.remove-icon:hover, .overview-close:hover { + background: transparent url(../images/fugue/cross-circle.png) no-repeat; +} +#close-icon { + background: transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px; +} +#close-icon:hover { + background: transparent url(../images/fugue/cross-circle.png) no-repeat; +} +#add-tracks-icon { + background: transparent url(../images/fugue/plus-button-bw.png) no-repeat; +} +#add-tracks-icon:hover { + background: transparent url(../images/fugue/plus-button.png) no-repeat; +} +#add-group-icon { + background: transparent url(../images/fugue/block--plus-bw.png) no-repeat; +} +#add-group-icon:hover { + background: transparent url(../images/fugue/block--plus.png) no-repeat; +} +#bookmarks-icon { + background: transparent url(../images/fugue/bookmarks-bw.png) no-repeat; +} +#bookmarks-icon:hover { + background: transparent url(../images/fugue/bookmarks.png) no-repeat; +} +#save-icon { + background: transparent url(../images/fugue/disk--arrow-bw.png) no-repeat; +} +#save-icon:hover { + background: transparent url(../images/fugue/disk--arrow.png) no-repeat; +} .child-track-icon { background:url('../images/fugue/arrow-000-small-bw.png') no-repeat; width: 30px; @@ -317,7 +387,6 @@ .delete-icon-container { float:right; } - .icon { display:inline-block; width:16px; diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -698,6 +698,8 @@ }); // Tooltips if ( $.fn.tipsy ) { + // FIXME: tipsy gravity cannot be updated, so need classes that specify N/S gravity and + // initialize each separately. $(".tooltip").tipsy( { gravity: 's' } ); } // Make popup menus. diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(R.prototype,r.prototype,z.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(ah,-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}ao.predisplay_actions();var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var 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T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var 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U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=A};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(V,Q,M,aa,B,U,J,G,F){V.textAlign="center";var T=this,A=[aa,B],P=0,W=0,S=0;ref_seq=this.ref_seq.data,char_width_px=V.canvas.manager.char_width_px;var 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g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var 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g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name==m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -37,7 +37,6 @@ }; })(); - /** * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first @@ -74,6 +73,7 @@ return overlap; }; + /** * Returns true if regions overlap. */ @@ -82,6 +82,74 @@ return (overlap !== BEFORE && overlap !== AFTER); }; +/** + * Returns a random color in hexadecimal format that is sufficiently different from a single color + * or set of colors. + * @param colors a color or list of colors in the format '#RRGGBB' + */ +var get_random_color = function(colors) { + // Default for colors is white. + if (!colors) { colors = "#ffffff" }; + + // If needed, create list of colors. + if ( typeof(colors) === "string" ) { + colors = [ colors ]; + } + + // Convert colors to numbers. + for (var i = 0; i < colors.length; i++) { + colors[i] = parseInt( colors[i].slice(1), 16 ); + } + + // -- Perceived brightness and difference formulas are from + // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast + + // Compute perceived color brightness (based on RGB-YIQ transformation): + var brightness = function(r, g, b) { + return ( (r * 299) + (g * 587) + (b * 114) ) / 1000; + }; + + // Compute color difference: + var difference = function(r1, g1, b1, r2, g2, b2) { + return ( Math.max(r1, r2) - Math.min(r1, r2) ) + + ( Math.max(g1, g2) - Math.min(g1, g2) ) + + ( Math.max(b1, b2) - Math.min(b1, b2) ); + }; + + // Create new random color. + var new_color, nr, ng, nb, + other_color, or, og, ob, + n_brightness, o_brightness, + diff, ok = false; + do { + // New color is never white b/c random in [0,1) + new_color = Math.random() * 0xffffff; + nr = new_color | 0xff0000; + ng = new_color | 0x00ff00; + nb = new_color | 0x0000ff; + n_brightness = brightness(nr, ng, nb); + ok = true; + for (var i = 0; i < colors.length; i++) { + other_color = colors[i]; + or = other_color | 0xff0000; + og = other_color | 0x00ff00; + ob = other_color | 0x0000ff; + o_brightness = brightness(or, og, ob); + diff = difference(nr, ng, nb, or, og, ob); + // Thresholds for brightness difference and color difference + // are from W3C link above. + if ( ( Math.abs(n_brightness - o_brightness) < 125 ) || + ( diff < 500 ) ) { + ok = false; + break; + } + } + } while (!ok); + + // Add 0x1000000 to left pad number with 0s. + return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6); +}; + // Encapsulate -- anything to be availabe outside this block is added to exports var trackster_module = function(require, exports) { @@ -463,7 +531,7 @@ // data is ready, it then replaces itself with the actual data entry = this.load_data(low, high, mode, resolution, extra_params); this.set_data(low, high, mode, entry); - return entry + return entry; }, /** "Deep" data request; used as a parameter for DataManager.get_more_data() */ DEEP_DATA_REQ: "deep", @@ -589,7 +657,6 @@ this.name = name; this.view = view; this.container = container; - this.drag_handle_class = drag_handle_class; this.config = new DrawableConfig({ track: this, params: [ @@ -601,6 +668,8 @@ } }); this.prefs = this.config.values; + this.drag_handle_class = drag_handle_class; + this.is_overview = false; }; extend(Drawable.prototype, { @@ -608,7 +677,7 @@ request_draw: function() {}, _draw: function() {}, to_json: function() {}, - make_name_popup_menu: function() {}, + update_track_icons: function() {}, /** * Set drawable name. */ @@ -750,14 +819,14 @@ is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - this.make_name_popup_menu(); + this.update_track_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { /** * Make popup menu for group. */ - make_name_popup_menu: function() { + update_track_icons: function() { var group = this; var group_dropdown = {}; @@ -852,7 +921,7 @@ // Overview (scrollbar and overview plot) at bottom this.overview = $("<div/>").addClass("overview").appendTo(this.bottom_container); this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview); - this.overview_close = $("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport); + this.overview_close = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport); this.overview_highlight = $("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport); this.overview_box_background = $("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport); this.overview_box = $("<div/>").addClass("overview-box").appendTo(this.overview_viewport); @@ -1195,13 +1264,14 @@ /** * Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks. */ + // FIXME: change method call so that track is first and additional parameters are optional. request_redraw: function(nodraw, force, clear_after, track) { var view = this, - // Either redrawing a single track or all view's tracks. + // Either redrawing a single drawable or all view's drawables. track_list = (track ? [track] : view.drawables), track_index; - + // Add/update tracks in track list to redraw list. var track; for (var i = 0; i < track_list.length; i++) { @@ -1318,42 +1388,44 @@ this.nav_container.width( this.container.width() ); this.request_redraw(); }, - /** Show a track in the overview. */ - set_overview: function(track) { - // Get data and draw tile. - $.when(track.get_overview_tile()).then(function(tile) { - // Update UI. - view.overview_viewport.find(".track-tile").remove(); + /** Show a Drawable in the overview. */ + set_overview: function(drawable) { + if (this.overview_drawable) { + // If drawable to be set as overview is already in overview, do nothing. + // Otherwise, remove overview. + if (this.overview_drawable.dataset_id === drawable.dataset_id) { + return; + } + this.overview_viewport.find(".track").remove(); + } + + // Set new overview. + var + overview_drawable = drawable.copy( { content_div: this.overview_viewport } ), + view = this; + overview_drawable.header_div.hide(); + overview_drawable.is_overview = true; + view.overview_drawable = overview_drawable; + this.overview_drawable.postdraw_actions = function() { + view.overview_highlight.show().height(view.overview_drawable.content_div.height()); + view.overview_viewport.height(view.overview_drawable.content_div.height() + view.overview_box.outerHeight()); view.overview_close.show(); - view.overview_viewport.append(tile.canvas); - view.overview_highlight.show().height(tile.canvas.height()); - view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight()); view.resize_window(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); - } - view.overview_track = track; - track.set_is_overview(true); - }); + }; + this.overview_drawable.init(); view.has_changes = true; }, /** Close and reset overview. */ reset_overview: function() { // Update UI. + $(".tipsy").remove(); this.overview_viewport.find(".track-tile").remove(); this.overview_viewport.height(this.default_overview_height); this.overview_box.height(this.default_overview_height); this.overview_close.hide(); this.overview_highlight.hide(); view.resize_window(); - - // Update view, track states. - if (view.overview_track) { - view.overview_track.set_is_overview(false); - } - view.overview_track = null; + view.overview_drawable = null; } }); @@ -2243,7 +2315,7 @@ * -------> ToolDataFeatureTrack * -------> VcfTrack */ -var Track = function(name, view, container, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2254,18 +2326,128 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; + + if (!Track.id_counter) { Track.id_counter = 0; } + this.id = Track.id_counter++; // // Create HTML element structure for track. // - if (!Track.id_counter) { Track.id_counter = 0; } - this.container_div = $("<div />").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative"); - if (!this.hidden) { + this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + + // Create and initialize track header and icons. + if (show_header) { this.header_div = $("<div class='track-header' />").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } - this.name_div = $("<div class='menubutton popup' />").appendTo(this.header_div); - this.name_div.text(this.name); - this.name_div.attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); + this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) + .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); + this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); + + // Track icons. + this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") + .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); + this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview") + .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); + this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") + .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div).hide(); + this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools") + .addClass("icon-button tools-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div).hide(); + this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") + .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) + .appendTo(this.icons_div); + var track = this; + + // Suppress double clicks in header so that they do not impact viz. + this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Clicking on settings icon opens track config. + this.settings_icon.click( function() { + var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + track.config.update_from_form( $(".dialog-box") ); + hide_modal(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + show_modal("Configure Track", track.config.build_form(), { + "Cancel": cancel_fn, + "OK": ok_fn + }); + }); + + this.overview_icon.click( function() { + track.view.set_overview(track); + }); + + this.filters_icon.click( function() { + // TODO: update tipsy text. + track.filters_div.toggle(); + track.filters_manager.reset_filters(); + }); + + this.tools_icon.click( function() { + // TODO: update tipsy text. + + track.dynamic_tool_div.toggle(); + + // Update track name. + if (track.dynamic_tool_div.is(":visible")) { + track.set_name(track.name + track.tool_region_and_parameters_str()); + } + else { + track.revert_name(); + } + // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. + $(".tipsy").remove(); + }); + + // Clicking on remove icon removes track. + this.remove_icon.click( function() { + // Tipsy for remove icon must be deleted when track is deleted. + $(".tipsy").remove(); + track.remove(); + }); + + // Set up behavior for modes popup. + if (track.display_modes !== undefined) { + if (track.mode_div === undefined) { + track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); + track.mode = init_mode; + track.mode_div.text(init_mode); + + var mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { track.change_mode(mode); }; + }(mode); + } + make_popupmenu(track.mode_div, mode_mapping); + } else { + track.mode_div.hide(); + } + + this.header_div.append( $("<div/>").css("clear", "both") ); + + // Set up config icon. + + // Show icons when users is hovering over track. + this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); + } } // @@ -2352,7 +2534,7 @@ } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; - track.make_name_popup_menu(); + track.update_track_icons(); } track.content_div.text(DATA_OK); if (track.view.chrom) { @@ -2367,14 +2549,18 @@ } } }); + + this.update_track_icons(); }, /** * Additional initialization required before drawing track for the first time. */ - predraw_init: function() {}, + predraw_init: function() {} }); -var TiledTrack = function(filters_list, tool_dict) { +var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) { + Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait); + var track = this, view = track.view; @@ -2387,54 +2573,33 @@ this.filters_available = false; this.filters_visible = false; this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); - this.is_overview = false; - if (track.hidden) { return; } + if (this.header_div) { + // + // Create filters div. + // + if (this.filters_manager) { + this.filters_div = this.filters_manager.parent_div + this.header_div.after(this.filters_div); + } - // - // Create filters div. - // - if (this.filters_manager) { - this.filters_div = this.filters_manager.parent_div - this.header_div.after(this.filters_div); - } - - // - // Create dynamic tool div. - // - if (this.tool) { - this.dynamic_tool_div = this.tool.parent_div; - this.header_div.after(this.dynamic_tool_div); - } - - // - // Create modes control. - // - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); + // + // Create dynamic tool div. + // + if (this.tool) { + this.dynamic_tool_div = this.tool.parent_div; + this.header_div.after(this.dynamic_tool_div); } } - - this.make_name_popup_menu(); }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** + * Returns a copy of the track. + */ + copy: function(container) { + return new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool); + }, + /** * Convert track to JSON object. */ to_json: function() { @@ -2461,87 +2626,31 @@ return track; }, /** - * Make popup menu for track name. + * Update track's buttons. */ - make_name_popup_menu: function() { + update_track_icons: function() { var track = this; - var track_dropdown = {}; - // - // Make track overview option. - // - track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { - if (track.is_overview) { - track.view.reset_overview(); - } - else { - track.view.set_overview(track); - } - }; - - // - // Edit config option. - // - track_dropdown["Edit configuration"] = function() { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - track.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Track", track.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); - }; - - // - // Show/hide filters option. + // Show/hide filter icon. // if (track.filters_available > 0) { - // Show/hide filters menu item. - var text = (track.filters_div.is(":visible") ? "Hide filters" : "Show filters"); - track_dropdown[text] = function() { - // Toggle filtering div, reset filters, and remake menu. - track.filters_visible = (track.filters_div.is(":visible")); - if (track.filters_visible) { - track.filters_manager.reset_filters(); - } - track.filters_div.toggle(); - track.make_name_popup_menu(); - }; + track.filters_icon.show(); + } + else { + track.filters_icon.hide(); } // - // Show/hide tool option. + // Show/hide tool icon. // if (track.tool) { - // Show/hide dynamic tool menu item. - var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool"); - track_dropdown[text] = function() { - // Set track name, toggle tool div, and remake menu. - if (!track.dynamic_tool_div.is(":visible")) { - track.set_name(track.name + track.tool_region_and_parameters_str()); - } - else { - menu_option_text = "Show dynamic tool"; - track.revert_name(); - } - track.dynamic_tool_div.toggle(); - track.make_name_popup_menu(); - }; + track.tools_icon.show(); } - + else { + track.tools_icon.hide(); + } + // // List chrom/contigs with data option. // @@ -2552,61 +2661,6 @@ }; } */ - - // - // Remove option. - // - track_dropdown.Remove = function() { - track.remove(); - }; - - make_popupmenu(track.name_div, track_dropdown); - }, - /** - * Set track's overview status. - */ - set_is_overview: function(is_overview) { - this.is_overview = is_overview; - this.make_name_popup_menu(); - }, - /** - * Returns a jQuery Deferred object that resolves to a Tile with track's overview. - * TODO: this should be the approach used when drawing any tile so that tile drawing is not blocking. - */ - get_overview_tile: function() { - var - track = this; - view = track.view, - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )), - view_width = view.container.width(), - // w_scale units are pixels per base. - w_scale = view_width / (view.max_high - view.max_low), - overview_tile = $.Deferred(); - $.when(track.data_manager.get_data(view.max_low, view.max_high, "Auto", resolution, track.data_url_extra_params)).then(function(overview_data) { - var - key = track._gen_tile_cache_key(view_width, w_scale, 0), - tile = track.tile_cache.get(key); - - // Draw tile if necessary. - if (!tile) { - tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale); - track.tile_cache.set(key, tile); - } - - // Always copy tile because it may need to be used in viz. - var - src_canvas = $(tile.canvas.find("canvas")), - new_canvas = src_canvas.clone(), - src_ctx = src_canvas.get(0).getContext("2d"), - tgt_ctx = new_canvas.get(0).getContext("2d"), - data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - // Need to undo offsets when placing image data. - tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0)); - new_tile = new Tile(track, -1, resolution, new_canvas); - overview_tile.resolve(new_tile); - }); - - return overview_tile; }, /** * Generate a key for the tile cache. @@ -2641,6 +2695,14 @@ w_scale = width / range, resolution = this.view.resolution, parent_element = $("<div style='position: relative;'></div>"); + + // For overview, adjust high, low, resolution, and w_scale. + if (this.is_overview) { + low = this.view.max_low; + high = this.view.max_high; + resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )); + w_scale = width / (view.max_high - view.max_low); + } if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); @@ -2751,7 +2813,7 @@ // Can't draw now, so trigger another redraw when the data is ready $.when( tile_data, seq_data ).then( function() { - view.request_redraw(); + view.request_redraw(false, false, false, track); }); // Indicate to caller that this tile could not be drawn @@ -2811,8 +2873,7 @@ tile.predisplay_actions(); // Position tile element, recalculate left position at display time - var range = this.view.high - this.view.low, - left = (tile.low - this.view.low) * w_scale; + var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale; if (this.left_offset) { left -= this.left_offset; } @@ -2849,8 +2910,7 @@ }); var LabelTrack = function (view, container) { - this.hidden = true; - Track.call(this, "label", view, container, {} ); + Track.call(this, "label", view, container, false, {} ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -2880,9 +2940,7 @@ }); var ReferenceTrack = function (view) { - this.hidden = true; - Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); - TiledTrack.call(this); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); view.reference_track = this; this.left_offset = 200; @@ -2909,7 +2967,7 @@ tile_length = DENSITY * resolution; if (w_scale > this.view.canvas_manager.char_width_px) { - if (seq === null) { + if (seq.data === null) { track.content_div.css("height", "0px"); return; } @@ -2934,8 +2992,7 @@ var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - Track.call( this, name, view, container, prefs ); - TiledTrack.call( this ); + TiledTrack.call( this, name, view, container, true, prefs ); this.min_height_px = 16; this.max_height_px = 400; @@ -2952,7 +3009,7 @@ track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, - { key: 'color', label: 'Color', type: 'color', default_value: 'black' }, + { key: 'color', label: 'Color', type: 'color', default_value: get_random_color() }, { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, @@ -3080,18 +3137,15 @@ // // Initialization. - // - - // FIXME: cleaner init needed; should just be able to call TiledTrack() - Track.call(this, name, view, container, prefs); - TiledTrack.call(this, filters, tool); + // + TiledTrack.call(this, name, view, container, true, prefs, filters, tool); // Define and restore track configuration. this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, - { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' }, + { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() }, { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, @@ -3203,7 +3257,7 @@ if (!track.filters_available) { track.filters_div.hide(); } - track.make_name_popup_menu(); + track.update_track_icons(); } } }, @@ -3345,9 +3399,12 @@ if (mode === "Auto") { if (result.dataset_type === "summary_tree") { mode = result.dataset_type; - } else if (result.extra_info === "no_detail") { + } + // HACK: use no_detail mode track is in overview to prevent overview from being too large. + else if (result.extra_info === "no_detail" || track.is_overview) { mode = "no_detail"; - } else { + } + else { // Choose b/t Squish and Pack. // Proxy measures for using Squish: // (a) error message re: limiting number of features shown; @@ -3478,7 +3535,7 @@ track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, - { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' }, + { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() }, { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, @@ -3495,7 +3552,7 @@ this.prefs = this.config.values; this.painter = painters.ReadPainter; - this.make_name_popup_menu(); + this.update_track_icons(); }; extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -114,7 +114,7 @@ // Set overview. var overview_track; for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].name == overview_track_name) { + if (view.drawables[i].name === overview_track_name) { view.set_overview(view.drawables[i]); break; } diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,10 +42,9 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )} <script type="text/javascript"> - // // Place URLs here so that url_for can be used to generate them. // @@ -113,6 +112,9 @@ }; $(function() { + // Manual tipsy config because default gravity is S and cannot be changed. + $(".menu-button").tipsy( {gravity: 'n'} ); + // Hide bookmarks by default right now. parent.force_right_panel("hide"); @@ -172,59 +174,62 @@ %endif // - // Make actions menu. + // Initialize icons. // - $("#viz-actions-button").css( "position", "relative" ); - make_popupmenu( $("#viz-actions-button"), { - "Add Tracks": add_tracks, - "Add Group": function() { - var group = new DrawableGroup("New Group", view, view); - view.add_drawable(group); - }, - "Save": function() { - // Show saving dialog box - show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); - - // Save bookmarks. - var bookmarks = []; - $(".bookmark").each(function() { - bookmarks[bookmarks.length] = { - position: $(this).children(".position").text(), - annotation: $(this).children(".annotation").text() - }; - }); - - var overview_track_name = (view.overview_track ? view.overview_track.name : null); - var payload = { - 'view': view.to_json(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks - }; - - $.ajax({ - url: "${h.url_for( action='save' )}", - type: "POST", - data: { - 'vis_id': view.vis_id, - 'vis_title': view.title, - 'dbkey': view.dbkey, - 'payload': JSON.stringify(payload) - }, - success: function(vis_id) { - view.vis_id = vis_id; - view.has_changes = false; - hide_modal(); - }, - error: function() { alert("Could not save visualization"); } - }); - }, - "Bookmarks": function() { - // HACK -- use style to determine if panel is hidden and hide/show accordingly. - parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); - }, - "Close": function() { window.location = "${h.url_for( controller='visualization', action='list' )}"; } + $("#add-tracks-icon").click( function() { add_tracks(); } ); + + $("#add-group-icon").click( function() { + view.add_drawable( new DrawableGroup("New Group", view, view) ); }); + $("#save-icon").click( function() { + // Show saving dialog box + show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); + + // Save bookmarks. + var bookmarks = []; + $(".bookmark").each(function() { + bookmarks[bookmarks.length] = { + position: $(this).children(".position").text(), + annotation: $(this).children(".annotation").text() + }; + }); + + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.name : null); + var payload = { + 'view': view.to_json(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + $.ajax({ + url: "${h.url_for( action='save' )}", + type: "POST", + data: { + 'vis_id': view.vis_id, + 'vis_title': view.title, + 'dbkey': view.dbkey, + 'payload': JSON.stringify(payload) + }, + success: function(vis_id) { + view.vis_id = vis_id; + view.has_changes = false; + hide_modal(); + }, + error: function() { alert("Could not save visualization"); } + }); + }); + + $("#bookmarks-icon").click( function() { + // HACK -- use style to determine if panel is hidden and hide/show accordingly. + parent.force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); + }); + + $("#close-icon").click( function() { + window.location = "${h.url_for( controller='visualization', action='list' )}"; + }); + $("#add-bookmark-button").click(function() { // Add new bookmark. var position = view.chrom + ":" + view.low + "-" + view.high, @@ -245,9 +250,14 @@ <div class="unified-panel-header-inner"><div style="float:left;" id="title"></div><div style="float: right"> - <a id="viz-actions-button" class='panel-header-button popup' href="javascript:void(0)" target="galaxy_main">${_('Actions')}</a> + <a id="add-tracks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add tracks"></a> + <a id="add-group-icon" class='icon-button menu-button' href="javascript:void(0);" title="Add new group"></a> + <a id="bookmarks-icon" class='icon-button menu-button' href="javascript:void(0);" title="Bookmarks"></a> + <a id="save-icon" class='icon-button menu-button' href="javascript:void(0);" title="Save"></a> + <a id="close-icon" class='icon-button menu-button' href="javascript:void(0);" title="Close"></a></div></div> + <div style="clear: both"></div></div><div id="browser-container" class="unified-panel-body"></div> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de test-data/picard_fastq_to_sam_out1.bam Binary file test-data/picard_fastq_to_sam_out1.bam has changed diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de test-data/picard_fastq_to_sam_out2.bam Binary file test-data/picard_fastq_to_sam_out2.bam has changed diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -295,6 +295,9 @@ <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><section name="NGS: Picard (beta)" id="picard_beta"> + <label text="Conversion" id="picard_conversion"/> + <tool file="picard/picard_FastqToSam.xml" /> + <tool file="picard/picard_SamToFastq.xml" /><label text="QC/Metrics for sam/bam" id="qcsambam"/><tool file="picard/picard_BamIndexStats.xml" /> @@ -390,7 +393,6 @@ <label text="Filtration" id="gatk_filtration" /><tool file="gatk/variant_filtration.xml" /> - <tool file="gatk/variant_filtration.xml" /><label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /><tool file="gatk/variant_recalibrator.xml" /> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/fastq/fastq_paired_end_deinterlacer.py --- a/tools/fastq/fastq_paired_end_deinterlacer.py +++ b/tools/fastq/fastq_paired_end_deinterlacer.py @@ -21,12 +21,14 @@ i = None skip_count = 0 found = {} - for i, mate1 in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ): + for i, read in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ): - if mate1.identifier in found: - del found[mate1.identifier] + if read.identifier in found: + del found[read.identifier] continue + mate1 = input.get( read.identifier ) + mate2 = input.get( joiner.get_paired_identifier( mate1 ) ) if mate2: diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -102,9 +102,9 @@ <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="select" label="Using reference genome"> - <!-- <options from_data_table="picard_indexes"> - <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> - </options> --> + <options from_data_table="picard_indexes"> + <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> + </options></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -159,9 +159,9 @@ <param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <!--<options from_data_table="picard_indexes"> - <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> - </options>--> + <options from_data_table="picard_indexes"> + <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> + </options></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -152,9 +152,9 @@ <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <!-- <options from_data_table="picard_indexes"> - <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> - </options> --> + <options from_data_table="picard_indexes"> + <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> + </options></param></when><when value="history"><!-- FIX ME!!!! --> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_AddOrReplaceReadGroups.xml --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -1,4 +1,4 @@ -<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.0"> +<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -15,7 +15,7 @@ #end if --output-format=$outputFormat --output=$outFile - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/AddOrReplaceReadGroups.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar" </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in" diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -1,4 +1,4 @@ -<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0"> +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -6,7 +6,7 @@ --bai-file "$input_file.metadata.bam_index" -t "$htmlfile" -d "$htmlfile.files_path" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar" </command><inputs><param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_FastqToSam.xml --- /dev/null +++ b/tools/picard/picard_FastqToSam.xml @@ -0,0 +1,144 @@ +<tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1"> + <description>creates an unaligned BAM file</description> + <requirements><requirement type="package">picard</requirement></requirements> + <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC + -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" + FASTQ="${input_fastq1}" + #if str( $input_fastq2) != "None": + FASTQ2="${input_fastq2}" + #end if + QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard + OUTPUT="${output_bam}" + READ_GROUP_NAME="${read_group_name}" + SAMPLE_NAME="${sample_name}" + #if $param_type.param_type_selector == "advanced": + #if str( $param_type.library_name ) != "": + LIBRARY_NAME="${param_type.library_name}" + #end if + #if str( $param_type.platform_unit ) != "": + PLATFORM_UNIT="${param_type.platform_unit}" + #end if + #if str( $param_type.platform ) != "": + PLATFORM="${param_type.platform}" + #end if + #if str( $param_type.sequencing_center ) != "": + SEQUENCING_CENTER="${param_type.sequencing_center}" + #end if + #if str( $param_type.predicted_insert_size ) != "": + PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}" + #end if + #if str( $param_type.description.value ) != "": + DESCRIPTION="${param_type.description}" + #end if + #if str( $param_type.run_date ) != "": + RUN_DATE="${param_type.run_date}" + #end if + #if str( $param_type.min_q ) != "": + MIN_Q="${param_type.min_q}" + #end if + #if str( $param_type.min_q ) != "": + MAX_Q="${param_type.max_q}" + #end if + SORT_ORDER="${param_type.sort_order}" + #else: + SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate + #end if + 2>&1 + || echo "Error running Picard FastqToSAM" >&2 + </command> + <inputs> + <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /><!-- confirm that fastqcssanger also works --> + <param name="input_fastq2" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." > + <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> + </options> + </param> + <param name="read_group_name" type="text" value="A" label="Read Group Name" /> + <param name="sample_name" type="text" value="unknown sample" label="Sample Name" /> + <conditional name="param_type"> + <param name="param_type_selector" type="select" label="Basic or Advanced options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </when> + <when value="advanced"> + <param name="library_name" type="text" value="" label="Library Name" /> + <param name="platform_unit" type="text" value="" label="Platform Unit" /> + <param name="platform" type="text" value="" label="Platform" /> + <param name="sequencing_center" type="text" value="" label="Sequencing Center" /> + <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" /> + <param name="description" type="text" value="" label="Description" /> + <param name="run_date" type="text" value="" label="Run Date" /> + <param name="min_q" type="integer" optional="True" value="0" label="Min Q" /> + <param name="max_q" type="integer" optional="True" value="93" label="Max Q" /> + <param name="sort_order" type="select" label="Sort order"> + <option value="coordinate" selected="True">coordinate</option> + <option value="queryname">queryname</option> + <option value="unsorted">unsorted</option> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" name="output_bam" /> + </outputs> + <tests> + <test> + <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> + <param name="input_fastq2" /> + <param name="read_group_name" value="A" /> + <param name="sample_name" value="unknown sample" /> + <param name="param_type_selector" value="basic" /> + <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> + </test> + <test> + <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> + <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> + <param name="read_group_name" value="A" /> + <param name="sample_name" value="unknown sample" /> + <param name="param_type_selector" value="basic" /> + <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> + </test> + </tests> + <help> +**What it does** + +Picard: FastqToSam converts FASTQ files to unaligned BAM files. + +------ + +Please cite the website "http://picard.sourceforge.net". + +------ + + +**Input formats** + +FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files. + +------ + +**Outputs** + +The output is in BAM format, see http://samtools.sourceforge.net for more details. + +------- + +**FastqToSam settings** + +This is list of FastqToSam options:: + + READ_GROUP_NAME=String Read group name Default value: A. This option can be set to 'null' to clear the default value. + SAMPLE_NAME=String Sample name to insert into the read group header Required. + LIBRARY_NAME=String The library name to place into the LB attribute in the read group header Default value: null. + PLATFORM_UNIT=String The platform unit (often run_barcode.lane) to insert into the read group header Default value: null. + PLATFORM=String The platform type (e.g. illumina, solid) to insert into the read group header Default value: null. + SEQUENCING_CENTER=String The sequencing center from which the data originated Default value: null. + PREDICTED_INSERT_SIZE=Integer Predicted median insert size, to insert into the read group header Default value: null. + DESCRIPTION=String Inserted into the read group header Default value: null. + </help> +</tool> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -1,4 +1,4 @@ -<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01"> +<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1"><command interpreter="python"> picard_wrapper.py --input="$input_file" @@ -20,7 +20,7 @@ --output-sam=$outFileBamMarked #end if #end if - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/" --picard-cmd="MarkDuplicates" </command><inputs> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -1,4 +1,4 @@ -<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.0"> +<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -15,7 +15,7 @@ --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat --output=$outFile - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar" </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered" diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_ReplaceSamHeader.xml --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -1,4 +1,4 @@ -<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.0"> +<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -6,7 +6,7 @@ -o $outFile --header-file $headerFile --output-format $outputFormat - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReplaceSamHeader.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReplaceSamHeader.jar" --tmpdir "${__new_file_path__}" </command><inputs> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/picard_SamToFastq.xml --- /dev/null +++ b/tools/picard/picard_SamToFastq.xml @@ -0,0 +1,157 @@ +<tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1"> + <description>creates a FASTQ file</description> + <requirements><requirement type="package">picard</requirement></requirements> + <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC + -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar" + INPUT="${input_sam}" + RE_REVERSE=${re_reverse} + INCLUDE_NON_PF_READS=${include_non_pf_reads} + #if str( $clipping_attribute ): + CLIPPING_ATTRIBUTE="${clipping_attribute}" + #end if + #if str( $clipping_action ): + CLIPPING_ACTION="${clipping_action}" + #end if + #if str( $read1_trim ): + READ1_TRIM="${read1_trim}" + #end if + #if str( $read1_max_bases_to_write ): + READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" + #end if + INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments} + + #if str( $output_per_read_group_selector ) == 'per_sam_file': + ##OUTPUT_PER_RG=false + FASTQ="${output_fastq1}" + + #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired': + SECOND_END_FASTQ="${output_fastq2}" + #if str( $single_paired_end_type.read2_trim ): + READ2_TRIM="${single_paired_end_type.read2_trim}" + #end if + #if str( $single_paired_end_type.read2_max_bases_to_write ): + READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}" + #end if + #end if + #else: + #raise Exception( 'Per Read Group not yet supported.' ) + OUTPUT_PER_RG=true + OUTPUT_DIR="./picard_sam_to_fastq_tmp_dir/" + #end if + 2>&1 + || echo "Error running SamToFastq" >&2 + </command> + <inputs> + <param name="input_sam" type="data" format="sam" label="SAM file" /> + <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." /> + <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." /> + <param name="output_per_read_group_selector" type="select" label="Output per read group"> + <option value="per_sam_file" selected="True">Per SAM file</option> + <!-- <option value="per_read_group">Per Read Group</option> --> + <validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator> + </param> + <conditional name="single_paired_end_type"> + <param name="single_paired_end_type_selector" type="select" label="Single or Paired end"> + <option value="single" selected="True">Single</option> + <option value="paired">Paired end</option> + </param> + <when value="single"> + <!-- nothing yet --> + </when> + <when value="paired"> + <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." /> + <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." /> + </when> + </conditional> + <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/> + <param name="include_non_pf_reads" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Include non-PF reads from the SAM file into the output FASTQ files."/> + <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM record should be clipped" help="Leave blank for null" /> + <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads" help="'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Leave blank for null" /> + <param name="include_non_primary_alignments" type="boolean" truevalue="true" falsevalue="false" checked="False" label="If true, include non-primary alignments in the output." help="Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments."/> + + </inputs> + <outputs> + <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" /> + <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" > + <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_sam" value="bfast_out1.sam" ftype="sam" /> + <param name="output_per_read_group_selector" value="per_sam_file" /> + <param name="single_paired_end_type_selector" value="single" /> + <param name="read1_trim" value="" /> + <param name="read1_max_bases_to_write" value="" /> + <param name="re_reverse" value="True" /> + <param name="include_non_pf_reads" value="False" /> + <param name="clipping_action" value="" /> + <param name="clipping_attribute" value="" /> + <param name="include_non_primary_alignments" value="False" /> + <output name="output_fastq1" file="random_phiX_1.fastqsanger"/> + </test> + <test> + <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" /> + <param name="output_per_read_group_selector" value="per_sam_file" /> + <param name="single_paired_end_type_selector" value="paired" /> + <param name="read1_trim" value="" /> + <param name="read1_max_bases_to_write" value="" /> + <param name="read2_trim" value="" /> + <param name="read2_max_bases_to_write" value="" /> + <param name="re_reverse" value="True" /> + <param name="include_non_pf_reads" value="False" /> + <param name="clipping_action" value="" /> + <param name="clipping_attribute" value="" /> + <param name="include_non_primary_alignments" value="False" /> + <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/><!-- 16 unaligned fastq blocks not present in original sam file --> + <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/><!-- 16 unaligned fastq blocks not present in original sam file --> + </test> + </tests> + <help> +**What it does** + +Picard: SamToFastq converts SAM files to FASTQ files. + +Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer. + +------ + +Please cite the website "http://picard.sourceforge.net". + +------ + + +**Input formats** + +FastqToSam accepts SAM input files, see http://samtools.sourceforge.net for more details. + +------ + +**Outputs** + +The output is in FASTQ format. If using Paired end data, 2 fastq files are created. + +------- + +**FastqToSam settings** + +This is list of SamToFastq options:: + + INPUT=File Input SAM/BAM file to extract reads from Required. + FASTQ=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) + SECOND_END_FASTQ=File Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) + OUTPUT_PER_RG=Boolean Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F) + OUTPUT_DIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null. + RE_REVERSE=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false} + INCLUDE_NON_PF_READS=Boolean Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} + CLIPPING_ATTRIBUTE=String The attribute that stores the position at which the SAM record should be clipped Default value: null. + CLIPPING_ACTION=String The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null. + READ1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value. + READ1_MAX_BASES_TO_WRITE=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null. + READ2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value. + READ2_MAX_BASES_TO_WRITE=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null. + INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} + + + </help> +</tool> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,8 +1,8 @@ -<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03"> +<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardFixMate.xml --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -1,8 +1,8 @@ -<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0"> +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1"><description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" - --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder" + --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FixMateInformation.jar" --sortorder "$sortOrder" </command><requirements><requirement type="package">picard</requirement></requirements><inputs> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardGCBiasMetrics.xml --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -1,8 +1,8 @@ -<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02"> +<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else: diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardHsMetrics.xml --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,10 +1,10 @@ -<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02"> +<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1"><description>for targeted resequencing data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CalculateHsMetrics.jar" </command><requirements><requirement type="package">picard</requirement></requirements> diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardInsertSize.xml --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,10 +1,10 @@ -<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" --histwidth "$histWidth" --minpct "$minPct" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs><param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardLibComplexity.xml --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -1,8 +1,8 @@ -<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01"> +<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs><param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" diff -r 603924d3abc3057def82337b53178ad48a71b1d1 -r 125d735c689ee60ad9bd9601c7a22738ba3523de tools/picard/rgPicardMarkDups.xml --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -1,8 +1,8 @@ -<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01"> +<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" </command><requirements><requirement type="package">picard</requirement></requirements><inputs> https://bitbucket.org/galaxy/galaxy-central/changeset/ab8fb6d1f56d/ changeset: ab8fb6d1f56d user: natefoo date: 2011-10-27 19:51:28 summary: merge affected #: 37 files diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1,10 +1,11 @@ """ Contains functionality needed in every web interface """ -import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess +import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, binascii from datetime import date, datetime, timedelta from time import strftime from galaxy import config, tools, web, util +from galaxy.util.hash_util import * from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * @@ -2484,3 +2485,32 @@ message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." error = True return error, message +def tool_shed_encode( val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val + a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) +def tool_shed_decode( value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test + # Restore from string + values = None + try: + values = simplejson.loads( value ) + except Exception, e: + log.debug( "Decoding json value from tool shed threw exception: %s" % str( e ) ) + if values is not None: + try: + return json_fix( values ) + except Exception, e: + log.debug( "Fixing decoded json value from tool shed threw exception: %s" % str( e ) ) + fixed_values = values + if values is None: + values = value + return values diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -4,8 +4,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch from galaxy.tools import json_fix -from galaxy.util.hash_util import * -import simplejson, binascii, logging +import logging log = logging.getLogger( __name__ ) from galaxy.actions.admin import AdminActions @@ -705,6 +704,13 @@ return trans.response.send_redirect( url ) @web.expose @web.require_admin + def find_workflows_in_tool_shed( self, trans, **kwd ): + tool_shed_url = kwd[ 'tool_shed_url' ] + galaxy_url = trans.request.host + url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url ) + return trans.response.send_redirect( url ) + @web.expose + @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = trans.request.host @@ -736,7 +742,7 @@ section_key = 'section_%s' % kwd[ 'tool_panel_section' ] tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. - repo_info_dict = self.__decode( repo_info_dict ) + repo_info_dict = tool_shed_decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() for name, repo_info_tuple in repo_info_dict.items(): @@ -1157,15 +1163,6 @@ section_str += ' </tool>\n' section_str += ' </section>\n' return section_str - def __decode( self, value ): - # Extract and verify hash - a, b = value.split( ":" ) - value = binascii.unhexlify( b ) - test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - assert a == test - # Restore from string - values = json_fix( simplejson.loads( value ) ) - return values ## ---- Utility methods ------------------------------------------------------- diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -663,7 +663,8 @@ vis.latest_revision = vis_rev session.add( vis_rev ) session.flush() - return trans.security.encode_id(vis.id) + encoded_id = trans.security.encode_id(vis.id) + return { "id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } @web.expose @web.require_login( "see all available libraries" ) diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -4,7 +4,7 @@ pkg_resources.require( "simplejson" ) pkg_resources.require( "SVGFig" ) import simplejson -import base64, httplib, urllib2, sgmllib, svgfig +import base64, httplib, urllib2, sgmllib, svgfig, urllib, urllib2 import math from galaxy.web.framework.helpers import time_ago, grids from galaxy.tools.parameters import * @@ -1092,13 +1092,35 @@ trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-Workflow-%s.ga" % ( sname ) trans.response.set_content_type( 'application/galaxy-archive' ) return stored_dict - @web.expose def import_workflow( self, trans, **kwd ): + """ + Import a workflow by reading an url, uploading a file, or receiving the textual + representation of a workflow. + """ url = kwd.get( 'url', '' ) + workflow_text = kwd.get( 'workflow_text', '' ) + webapp = kwd.get( 'webapp', 'galaxy' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - if kwd.get( 'import_button', False ): + import_button = kwd.get( 'import_button', False ) + tool_shed_url = kwd.get( 'tool_shed_url', '' ) + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + # The workflow_name parameter is in the request only if the import originated + # from a Galaxy tool shed, in which case the value was encoded. + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = tool_shed_decode( workflow_name ) + if tool_shed_url and not import_button: + # Use urllib (send another request to the tool shed) to retrieve the workflow. + workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + response = urllib2.urlopen( workflow_url ) + workflow_text = response.read() + response.close() + workflow_text = workflow_text + import_button = True + if import_button: workflow_data = None if url: # Load workflow from external URL @@ -1108,6 +1130,8 @@ except Exception, e: message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) status = 'error' + elif workflow_text: + workflow_data = workflow_text else: # Load workflow from browsed file. file_data = kwd.get( 'file_data', '' ) @@ -1175,6 +1199,13 @@ else: # TODO: Figure out what to do here... pass + if tool_shed_url: + # We've received the textual representation of a workflow from a Galaxy tool shed. + message = "This workflow has been successfully imported into your local Galaxy instance." + # TODO: support https in the following url. + url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + return trans.response.send_redirect( url ) return self.list( trans ) return trans.fill_template( "workflow/import.mako", url=url, diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -35,6 +35,8 @@ self.tag_handler = CommunityTagHandler() # Tool data tables self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + # The tool shed has no toolbox, but this attribute is still required. + self.toolbox = None # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -332,13 +332,13 @@ if 'tools' in metadata: metadata_str += '<b>Tools:</b><br/>' for tool_metadata_dict in metadata[ 'tools' ]: - metadata_str += '%s <b>%s</b><br/>' % \ - ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + metadata_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], + tool_metadata_dict[ 'version' ] ) if 'workflows' in metadata: metadata_str += '<b>Workflows:</b><br/>' for workflow_metadata_dict in metadata[ 'workflows' ]: - metadata_str += '%s <b>%s</b><br/>' % \ - ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) + metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ], + workflow_metadata_dict[ 'format-version' ] ) return metadata_str class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,8 +1,9 @@ -import os, string, socket, logging +import os, string, socket, logging, simplejson, binascii from time import strftime from datetime import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.hash_util import * from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -126,23 +127,18 @@ def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything except the - workflow steps in the database. + to the received exported_workflow_dict. Store everything in the database. """ - workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], - 'name' :exported_workflow_dict[ 'name' ], - 'annotation' : exported_workflow_dict[ 'annotation' ], - 'format-version' : exported_workflow_dict[ 'format-version' ] } if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( workflow_dict ) + metadata_dict[ 'workflows' ].append( exported_workflow_dict ) else: - metadata_dict[ 'workflows' ] = [ workflow_dict ] + metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] return metadata_dict def new_workflow_metadata_required( trans, id, metadata_dict ): """ - TODO: Currently everything about an exported workflow except the name is hard-coded, so - there's no real way to differentiate versions of exported workflows. If this changes at - some future time, this method should be enhanced accordingly... + Currently everything about an exported workflow except the name is hard-coded, so there's + no real way to differentiate versions of exported workflows. If this changes at some future + time, this method should be enhanced accordingly. """ if 'workflows' in metadata_dict: repository_metadata = get_latest_repository_metadata( trans, id ) @@ -425,18 +421,20 @@ trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - message = "Change set revision '%s' includes no tools or exported workflows for which metadata can be set." % str( changeset_revision ) + message = "Revision '%s' includes no tools or exported workflows for which metadata can be defined " % str( changeset_revision ) + message += "so this revision cannot be automatically installed into a local Galaxy instance." status = "error" else: # change_set is None - message = "Repository does not include change set revision '%s'." % str( changeset_revision ) + message = "This repository does not include revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: if metadata_dict: - message = "Metadata was defined for some items in change set revision '%s'. " % str( changeset_revision ) + message = "Metadata was defined for some items in revision '%s'. " % str( changeset_revision ) message += "Correct the following problems if necessary and reset metadata.<br/>" else: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) + message = "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( changeset_revision ) + message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" for itc_tup in invalid_files: tool_file, exception_msg = itc_tup if exception_msg.find( 'No such file or directory' ) >= 0: @@ -619,3 +617,24 @@ selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field +def encode( val ): + if isinstance( val, dict ): + value = simplejson.dumps( val ) + else: + value = val + a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + b = binascii.hexlify( value ) + return "%s:%s" % ( a, b ) +def decode( value ): + # Extract and verify hash + a, b = value.split( ":" ) + value = binascii.unhexlify( b ) + test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) + assert a == test + # Restore from string + try: + values = json_fix( simplejson.loads( value ) ) + except Exception, e: + # We do not have a json string + values = value + return values diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,7 +9,6 @@ from galaxy.webapps.community.model import directory_hash_id from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string -from galaxy.util.hash_util import * from galaxy.model.orm import * from common import * from mercurial import hg, ui, patch, commands @@ -232,7 +231,7 @@ return repository_metadata.repository.user.username return 'no user' # Grid definition - title = "Repositories with matching tools" + title = "Matching repositories" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' default_sort_key = "Repository.name" @@ -376,6 +375,83 @@ # Render the list view return self.valid_repository_list_grid( trans, **kwd ) @web.expose + def find_workflows( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + if 'operation' in kwd: + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) + if operation == "install": + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + encoded_repo_info_dict = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + # TODO: support https in the following url. + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s' % \ + ( galaxy_url, trans.request.host, webapp, encoded_repo_info_dict ) + return trans.response.send_redirect( url ) + else: + # This can only occur when there is a multi-select grid with check boxes and an operation, + # and the user clicked the operation button without checking any of the check boxes. + return trans.show_error_message( "No items were selected." ) + workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if workflow_names: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if webapp == 'galaxy': + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions + install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( self.__stringify( workflow_names ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching workflows" + return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + webapp=webapp, + workflow_name=self.__stringify( workflow_names ), + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + @web.expose def find_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -422,7 +498,7 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = self.__search_repository_metadata( trans, tool_ids, tool_names, tool_versions, exact_matches_checked ) + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view @@ -431,7 +507,9 @@ global_actions = [ grids.GridAction( "Browse valid repositories", dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ) ] + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] @@ -440,6 +518,7 @@ else: kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching tools" return self.matched_repository_list_grid( trans, **kwd ) else: message = "No search performed - each field must contain the same number of comma-separated items." @@ -453,59 +532,76 @@ exact_matches_check_box=exact_matches_check_box, message=message, status=status ) - def __search_repository_metadata( self, trans, tool_ids, tool_names, tool_versions, exact_matches_checked ): + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ): match_tuples = [] ok = True for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): metadata = repository_metadata.metadata - tools = metadata[ 'tools' ] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + if tool_ids or tool_names or tool_versions: + if 'tools' in metadata: + tools = metadata[ 'tools' ] + else: + tools = [] + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + if workflow_names: + if 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + else: + workflows = [] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name=workflow_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False return ok, match_tuples + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name=None ): + workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() + return ( workflow_name == workflow_dict_workflow_name ) or \ + ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -588,15 +684,7 @@ changeset_revision = repository_metadata.changeset_revision repository_clone_url = generate_clone_url( trans, repository_id ) repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - return self.__encode( repo_info_dict ) - def __encode( self, val ): - if isinstance( val, dict ): - value = simplejson.dumps( val ) - else: - value = val - a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value ) - b = binascii.hexlify( value ) - return "%s:%s" % ( a, b ) + return encode( repo_info_dict ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -607,8 +695,10 @@ changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None revision_label = get_revision_label( trans, repository, changeset_revision ) changeset_revision_select_field = build_changeset_revision_select_field( trans, @@ -617,6 +707,7 @@ add_id_to_name=False ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, @@ -636,7 +727,7 @@ changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repo_info_dict = {} repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) - encoded_repo_info_dict = self.__encode( repo_info_dict ) + encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. # TODO: support https in the following url. url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repo_info_dict=%s' % \ @@ -1159,8 +1250,10 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None is_malicious = change_set_is_malicious( trans, id, repository.tip ) if is_malicious: @@ -1172,6 +1265,7 @@ return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, @@ -1299,9 +1393,11 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: + repository_metadata_id = None metadata = None is_malicious = False if is_malicious: @@ -1321,6 +1417,7 @@ allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/controllers/workflow.py --- /dev/null +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -0,0 +1,395 @@ +import pkg_resources +pkg_resources.require( "simplejson" ) +pkg_resources.require( "SVGFig" ) +import os, logging, ConfigParser, tempfile, shutil, svgfig +from galaxy.webapps.community import model +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.util.json import from_json_string, to_json_string +from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory +from galaxy.tools import DefaultToolState +from galaxy.web.controllers.workflow import attach_ordered_steps +from galaxy.model.orm import * +from common import * + +class RepoInputDataModule( InputDataModule ): + + type = "data_input" + name = "Input dataset" + + @classmethod + def new( Class, trans, tools_metadata=None, tool_id=None ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + return module + @classmethod + def from_dict( Class, trans, d, tools_metadata=None, secure=True ): + module = Class( trans ) + state = from_json_string( d[ "tool_state" ] ) + module.state = dict( name=state.get( "name", "Input Dataset" ) ) + return module + @classmethod + def from_workflow_step( Class, trans, tools_metadata, step ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + if step.tool_inputs and "name" in step.tool_inputs: + module.state[ 'name' ] = step.tool_inputs[ 'name' ] + return module + +class RepoToolModule( ToolModule ): + + type = "tool" + + def __init__( self, trans, tools_metadata, tool_id ): + self.trans = trans + self.tools_metadata = tools_metadata + self.tool_id = tool_id + self.tool = None + for tool_dict in tools_metadata: + if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: + self.tool = load_tool( trans, os.path.abspath( tool_dict[ 'tool_config' ] ) ) + self.post_job_actions = {} + self.workflow_outputs = [] + self.state = None + self.errors = None + @classmethod + def new( Class, trans, tools_metadata, tool_id=None ): + module = Class( trans, tools_metadata, tool_id ) + module.state = module.tool.new_state( trans, all_pages=True ) + return module + @classmethod + def from_dict( Class, trans, d, tools_metadata, secure=True ): + tool_id = d[ 'tool_id' ] + module = Class( trans, tools_metadata, tool_id ) + module.state = DefaultToolState() + if module.tool is not None: + module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = d.get( "tool_errors", None ) + return module + @classmethod + def from_workflow_step( Class, trans, tools_metadata, step ): + module = Class( trans, tools_metadata, step.tool_id ) + module.state = DefaultToolState() + if module.tool: + module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + else: + module.state.inputs = {} + module.errors = step.tool_errors + return module + def get_data_inputs( self ): + data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_inputs.append( dict( name=prefixed_name, + label=prefixed_label, + extensions=input.extensions ) ) + if self.tool: + visit_input_values( self.tool.inputs, self.state.inputs, callback ) + return data_inputs + def get_data_outputs( self ): + data_outputs = [] + if self.tool: + data_inputs = None + for name, tool_output in self.tool.outputs.iteritems(): + if tool_output.format_source != None: + # Default to special name "input" which remove restrictions on connections + formats = [ 'input' ] + if data_inputs == None: + data_inputs = self.get_data_inputs() + # Find the input parameter referenced by format_source + for di in data_inputs: + # Input names come prefixed with conditional and repeat names separated by '|', + # so remove prefixes when comparing with format_source. + if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + formats = di[ 'extensions' ] + else: + formats = [ tool_output.format ] + for change_elem in tool_output.change_format: + for when_elem in change_elem.findall( 'when' ): + format = when_elem.get( 'format', None ) + if format and format not in formats: + formats.append( format ) + data_outputs.append( dict( name=name, extensions=formats ) ) + return data_outputs + +class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): + self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): + """Return module for type and (optional) tool_id intialized with new / default state.""" + assert type in self.module_types + return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, d, **kwargs ): + """Return module initialized from the data in dictionary `d`.""" + type = d[ 'type' ] + assert type in self.module_types + return self.module_types[ type ].from_dict( trans, d, **kwargs ) + def from_workflow_step( self, trans, tools_metadata, step ): + """Return module initialized from the WorkflowStep object `step`.""" + type = step.type + return self.module_types[ type ].from_workflow_step( trans, tools_metadata, step ) + +module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + +class WorkflowController( BaseUIController ): + @web.expose + def view_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + repository=repository, + changeset_revision=repository_metadata.changeset_revision, + repository_metadata_id=repository_metadata_id, + workflow_name=workflow_name, + webapp=webapp, + message=message, + status=status ) + @web.expose + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + metadata = repository_metadata.metadata + workflow_name = decode( workflow_name ) + for workflow_dict in metadata[ 'workflows' ]: + if workflow_dict[ 'name' ] == workflow_name: + break + if 'tools' in metadata: + tools_metadata = metadata[ 'tools' ] + else: + tools_metadata = [] + workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata ) + data = [] + canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) + text = svgfig.SVG( "g" ) + connectors = svgfig.SVG( "g" ) + boxes = svgfig.SVG( "g" ) + svgfig.Text.defaults[ "font-size" ] = "10px" + in_pos = {} + out_pos = {} + margin = 5 + # Spacing between input/outputs. + line_px = 16 + # Store px width for boxes of each step. + widths = {} + max_width, max_x, max_y = 0, 0, 0 + for step in workflow.steps: + step.upgrade_messages = {} + module = module_factory.from_workflow_step( trans, tools_metadata, step ) + tool_errors = module.type == 'tool' and not module.tool + module_data_inputs = self.__get_data_inputs( step, module ) + module_data_outputs = self.__get_data_outputs( step, module, workflow.steps ) + step_dict = { + 'id' : step.order_index, + 'data_inputs' : module_data_inputs, + 'data_outputs' : module_data_outputs, + 'position' : step.position, + 'tool_errors' : tool_errors + } + input_conn_dict = {} + for conn in step.input_connections: + input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict[ 'input_connections' ] = input_conn_dict + data.append( step_dict ) + x, y = step.position[ 'left' ], step.position[ 'top' ] + count = 0 + module_name = self.__get_name( module, missing_tool_tups ) + max_len = len( module_name ) * 1.5 + text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) + y += 45 + for di in module_data_inputs: + cur_y = y + count * line_px + if step.order_index not in in_pos: + in_pos[ step.order_index ] = {} + in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( di[ 'label' ] ) ) + if len( module.get_data_inputs() ) > 0: + y += 15 + for do in module_data_outputs: + cur_y = y + count * line_px + if step.order_index not in out_pos: + out_pos[ step.order_index ] = {} + out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( do['name' ] ) ) + widths[ step.order_index ] = max_len * 5.5 + max_x = max( max_x, step.position[ 'left' ] ) + max_y = max( max_y, step.position[ 'top' ] ) + max_width = max( max_width, widths[ step.order_index ] ) + for step_dict in data: + tool_unavailable = step_dict[ 'tool_errors' ] + width = widths[ step_dict[ 'id' ] ] + x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] + if tool_unavailable: + fill = "#EBBCB2" + else: + fill = "#EBD9B2" + boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) + box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin + # Draw separator line. + if len( step_dict[ 'data_inputs' ] ) > 0: + box_height += 15 + sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 + text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) + # Define an input/output box. + boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): + in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] + out_conn_pos = out_pos[ output_dict[ 'id' ] ][ output_dict[ 'output_name' ] ] + adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + text.append( svgfig.SVG( "circle", + cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, + cy=out_conn_pos[ 1 ] - margin, + r = 5, + fill="#ffffff" ) ) + connectors.append( svgfig.Line( adjusted[ 0 ], + adjusted[ 1 ] - margin, + in_coords[ 0 ] - 10, + in_coords[ 1 ], + arrow_end = "true" ).SVG() ) + canvas.append( connectors ) + canvas.append( boxes ) + canvas.append( text ) + width, height = ( max_x + max_width + 50 ), max_y + 300 + canvas[ 'width' ] = "%s px" % width + canvas[ 'height' ] = "%s px" % height + canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + trans.response.set_content_type( "image/svg+xml" ) + return canvas.standalone_xml() + def __get_name( self, module, missing_tool_tups ): + module_name = module.get_name() + if module.type == 'tool' and module_name == 'unavailable': + for missing_tool_tup in missing_tool_tups: + missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup + if missing_tool_id == module.tool_id: + module_name = '%s' % missing_tool_name + return module_name + def __get_data_inputs( self, step, module ): + if module.type == 'tool': + if module.tool: + return module.get_data_inputs() + else: + data_inputs = [] + for wfsc in step.input_connections: + data_inputs_dict = {} + data_inputs_dict[ 'extensions' ] = [ '' ] + data_inputs_dict[ 'name' ] = wfsc.input_name + data_inputs_dict[ 'label' ] = 'Unknown' + data_inputs.append( data_inputs_dict ) + return data_inputs + return module.get_data_inputs() + def __get_data_outputs( self, step, module, steps ): + if module.type == 'tool': + if module.tool: + return module.get_data_outputs() + else: + data_outputs = [] + data_outputs_dict = {} + data_outputs_dict[ 'extensions' ] = [ 'input' ] + found = False + for workflow_step in steps: + for wfsc in workflow_step.input_connections: + if step.name == wfsc.output_step.name: + data_outputs_dict[ 'name' ] = wfsc.output_name + found = True + break + if found: + break + if not found: + # We're at the last step of the workflow. + data_outputs_dict[ 'name' ] = 'output' + data_outputs.append( data_outputs_dict ) + return data_outputs + return module.get_data_outputs() + def __workflow_from_dict( self, trans, data, tools_metadata ): + """Creates and returns workflow object from a dictionary.""" + trans.workflow_building_mode = True + workflow = model.Workflow() + workflow.name = data[ 'name' ] + workflow.has_errors = False + steps = [] + # Keep ids for each step that we need to use to make connections. + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the tool shed repository. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for key, step_dict in data[ 'steps' ].iteritems(): + # Create the model class for the step + step = model.WorkflowStep() + step.name = step_dict[ 'name' ] + step.position = step_dict[ 'position' ] + module = module_factory.from_dict( trans, step_dict, tools_metadata=tools_metadata, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the current repository. + step.tool_errors = 'unavailable' + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily. + step.temp_input_connections = step_dict[ 'input_connections' ] + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) + steps.append( step ) + steps_by_external_id[ step_dict[ 'id' ] ] = step + # Second pass to deal with connections between steps. + for step in steps: + # Input connections. + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + output_step = steps_by_external_id[ conn_dict[ 'id' ] ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_step = output_step + conn.output_name = conn_dict[ 'output_name' ] + step.input_connections.append( conn ) + del step.temp_input_connections + # Order the steps if possible. + attach_ordered_steps( workflow, steps ) + return workflow, missing_tool_tups + @web.expose + def import_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + workflows = repository_metadata.metadata[ 'workflows' ] + workflow_data = None + for workflow_data in workflows: + if workflow_data[ 'name' ] == workflow_name: + break + if workflow_data: + if kwd.get( 'open_for_url', False ): + tmp_fd, tmp_fname = tempfile.mkstemp() + to_file = open( tmp_fname, 'wb' ) + to_file.write( to_json_string( workflow_data ) ) + return open( tmp_fname ) + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + # TODO: support https in the following url. + url = 'http://%s/workflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ + ( galaxy_url, trans.request.host, repository_metadata_id, encode( workflow_name ), webapp ) + return trans.response.send_redirect( url ) + return trans.response.send_redirect( web.url_for( controller='workflow', + action='view_workflow', + message=message, + status=status ) ) diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -204,6 +204,34 @@ self.value = None self.user_value = None +class Workflow( object ): + def __init__( self ): + self.user = None + self.name = None + self.has_cycles = None + self.has_errors = None + self.steps = [] + +class WorkflowStep( object ): + def __init__( self ): + self.id = None + self.type = None + self.name = None + self.tool_id = None + self.tool_inputs = None + self.tool_errors = None + self.position = None + self.input_connections = [] + #self.output_connections = [] + self.config = None + +class WorkflowStepConnection( object ): + def __init__( self ): + self.output_step = None + self.output_name = None + self.input_step = None + self.input_name = None + ## ---- Utility methods ------------------------------------------------------- def sort_by_attr( seq, attr ): """ diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -205,14 +205,14 @@ def from_workflow_step( Class, trans, step ): tool_id = step.tool_id install_tool_id = None - if tool_id not in trans.app.toolbox.tools_by_id: + if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id: # The id value of tools installed from a Galaxy tool shed is a guid, but # these tool's old_id attribute should contain what we're looking for. for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): if tool_id == available_tool.old_id: install_tool_id = available_tool_id break - if tool_id in trans.app.toolbox.tools_by_id or install_tool_id: + if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id: module = Class( trans, tool_id ) module.state = DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -247,7 +247,9 @@ action_arguments = None n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) def get_name( self ): - return self.tool.name + if self.tool: + return self.tool.name + return 'unavailable' def get_tool_id( self ): return self.tool_id def get_tool_version( self ): diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1189,6 +1189,10 @@ } }, go_to: function(str) { + // Preprocess str to remove spaces and commas. + str = str.replace(/ |,/g, ""); + + // Go to new location. var view = this, new_low, new_high, @@ -1199,8 +1203,8 @@ if (pos !== undefined) { try { var pos_split = pos.split("-"); - new_low = parseInt(pos_split[0].replace(/,/g, ""), 10); - new_high = parseInt(pos_split[1].replace(/,/g, ""), 10); + new_low = parseInt(pos_split[0], 10); + new_high = parseInt(pos_split[1], 10); } catch (e) { return false; } diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -744,7 +744,7 @@ %if grid.global_actions: <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: + %if len( grid.global_actions ) < 3: %for action in grid.global_actions: <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a></li> %endfor diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -96,7 +96,7 @@ display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) %> %if data.purged: - <span class="icon-button display_disabled tooltip" title="Cannoy display datasets removed from disk"></span> + <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span> %else: <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" %if for_editing: @@ -150,6 +150,9 @@ %endif </div> %elif data_state == "error": + %if not data.purged: + <div>${data.get_size( nice_size=True )}</div> + %endif <div> An error occurred running this job: <i>${data.display_info().strip()}</i></div> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -212,10 +212,14 @@ 'dbkey': view.dbkey, 'payload': JSON.stringify(payload) }, - success: function(vis_id) { - view.vis_id = vis_id; + dataType: "json", + success: function(vis_info) { + hide_modal(); + view.vis_id = vis_info.vis_id; view.has_changes = false; - hide_modal(); + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url); }, error: function() { alert("Could not save visualization"); } }); diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -44,6 +44,20 @@ <div class="page-container" style="padding: 10px;"><div class="toolMenu"><div class="toolSectionList"> + %if repository_metadata: + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Search + </div> + <div class="toolSectionBody"> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a> + </div> + </div> + %endif <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repositories @@ -61,11 +75,6 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> %endif - %if repository_metadata: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> - </div> - %endif </div></div><div class="toolSectionBody"> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,8 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_tools_and_workflows( metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> + <% from galaxy.webapps.community.controllers.common import encode, decode %> %if metadata or can_set_metadata: <p/><div class="toolForm"> @@ -160,14 +161,34 @@ <table class="grid"><tr><td><b>name</b></td> + <td><b>steps</b></td><td><b>format-version</b></td><td><b>annotation</b></td></tr> %for workflow_dict in workflow_dicts: + <% + workflow_name = workflow_dict[ 'name' ] + if 'steps' in workflow_dict: + ## Initially steps were not stored in the metadata record. + steps = workflow_dict[ 'steps' ] + else: + steps = [] + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %><tr> - <td>${workflow_dict[ 'name' ]}</td> - <td>${workflow_dict[ 'format-version' ]}</td> - <td>${workflow_dict[ 'annotation' ]}</td> + <td> + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a> + </td> + <td> + %if 'steps' in workflow_dict: + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td></tr> %endfor </table> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -14,6 +14,7 @@ <br/><br/><ul class="manage-table-actions"><li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li></ul> %endif diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/find_workflows.mako --- /dev/null +++ b/templates/webapps/community/repository/find_workflows.mako @@ -0,0 +1,53 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +%if webapp == 'galaxy': + <br/><br/> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a></li> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + </ul> +%endif + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Search repositories for workflows</div> + <div class="toolFormBody"> + <div class="form-row"> + Enter a workflow name to find repositories that contain workflows matching the search criteria.<br/><br/> + Comma-separated strings may be entered to expand search criteria. + </div> + <div style="clear: both"></div> + <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" > + <div style="clear: both"></div> + <div class="form-row"> + <label>Workflow name:</label> + <input name="workflow_name" type="textfield" value="${workflow_name}" size="40"/> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Exact matches only:</label> + ${exact_matches_check_box.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Check the box to match text exactly (text case doesn't matter as all strings are forced to lower case). + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" value="Search repositories"/> + </div> + </form> + </div> +</div> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -184,7 +184,7 @@ </form></div></div> -${render_repository_tools_and_workflows( metadata, can_set_metadata=True )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -69,6 +69,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div></ul> @@ -103,4 +104,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( metadata, webapp=webapp )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -116,6 +116,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %else: %if is_new: diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -99,6 +99,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %endif </ul> @@ -185,7 +186,7 @@ %endif </div></div> -${render_repository_tools_and_workflows( metadata, webapp=webapp )} +${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} %if repository.categories: <p/><div class="toolForm"> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -39,6 +39,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></div> %else: %if is_new: diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/community/repository/view_workflow.mako --- /dev/null +++ b/templates/webapps/community/repository/view_workflow.mako @@ -0,0 +1,105 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/community/common/common.mako" import="*" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /> + +<% + from galaxy.web.framework.helpers import time_ago + from galaxy.webapps.community.controllers.common import encode + + in_tool_shed = webapp == 'community' + is_admin = trans.user_is_admin() + is_new = repository.is_new + can_manage = is_admin or trans.user == repository.user + can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user + can_push = in_tool_shed and trans.app.security_agent.can_push( trans.user, repository ) + can_upload = can_push + can_download = in_tool_shed and not is_new and ( not is_malicious or can_push ) + can_browse_contents = in_tool_shed and not is_new + can_set_metadata = in_tool_shed and not is_new + can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user + can_view_change_log = in_tool_shed and not is_new + if can_push: + browse_label = 'Browse or delete repository files' + else: + browse_label = 'Browse repository files' +%> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )"> + <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp ) %> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> +</%def> + +<br/><br/> +<ul class="manage-table-actions"> + %if in_tool_shed: + %if is_new and can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + %if can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + %endif + %if can_manage: + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> + %else: + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + %endif + %if can_view_change_log: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + %endif + %if can_rate: + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> + %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + %endif + %if can_contact_owner: + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + %endif + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> + %endif + </div> + %endif + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install repository to local Galaxy</a></li> + </div> + <li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="toolshed-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + </div> + %endif +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolFormTitle">${workflow_name}</div> +<div class="form-row"> + <b>Boxes are red when tools are not available in this repository</b> + <div class="toolParamHelp" style="clear: both;"> + (this page displays SVG graphics) + </div> +</div> +<br clear="left"/> + +${render_workflow( repository_metadata_id, workflow_name, webapp )} diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -73,7 +73,7 @@ <div class="toolSectionTitle">Tool sheds</div><div class="toolSectionBody"><div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Browse tool sheds</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_sheds' )}" target="galaxy_main">Search and browse tool sheds</a></div></div></div> %endif diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/webapps/galaxy/admin/tool_sheds.mako --- a/templates/webapps/galaxy/admin/tool_sheds.mako +++ b/templates/webapps/galaxy/admin/tool_sheds.mako @@ -27,6 +27,7 @@ <div popupmenu="dataset-${shed_id}-popup"><a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed', tool_shed_url=url )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='admin', action='find_tools_in_tool_shed', tool_shed_url=url )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='admin', action='find_workflows_in_tool_shed', tool_shed_url=url )}">Search for workflows</a></div></td></tr> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -1,7 +1,7 @@ <%inherit file="/display_base.mako"/><%namespace file="/display_common.mako" import="render_message" /> -<%! +<% from galaxy.tools.parameters import DataToolParameter, RuntimeValue from galaxy.web import form_builder %> @@ -82,7 +82,17 @@ %for i, step in enumerate( steps ): <tr><td> %if step.type == 'tool' or step.type is None: - <% tool = app.toolbox.tools_by_id[step.tool_id] %> + <% + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break + %><div class="toolForm"><div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div><div class="toolFormBody"> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 templates/workflow/run.mako --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -363,7 +363,17 @@ %endif %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: - <% tool = app.toolbox.tools_by_id[step.tool_id] %> + <% + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break + %><input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}"><div class="toolForm"><div class="toolFormTitle"> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -138,6 +138,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -147,7 +148,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -107,6 +107,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -116,7 +117,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -103,6 +103,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -112,7 +113,9 @@ </param></when><when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -117,6 +117,7 @@ <when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -126,7 +127,9 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -7,8 +7,6 @@ --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): - ${dir( $input_bam.input_bam )} - ${dir( $input_bam.input_bam.dataset )} -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index #end for @@ -137,6 +135,7 @@ <repeat name="input_bams" title="Sample BAM file" min="1"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat> @@ -148,7 +147,9 @@ </when><when value="history"><!-- FIX ME!!!! --><repeat name="input_bams" title="Sample BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="input_bam" type="data" format="bam" label="BAM file" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param></repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -145,6 +145,7 @@ <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /><param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" /> + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> @@ -156,7 +157,9 @@ <when value="history"><!-- FIX ME!!!! --><param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" /> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" > + <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> + </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -42,11 +42,11 @@ || echo "Error running SamToFastq" >&2 </command><inputs> - <param name="input_sam" type="data" format="sam" label="SAM file" /> + <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" /><param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." /><param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." /><param name="output_per_read_group_selector" type="select" label="Output per read group"> - <option value="per_sam_file" selected="True">Per SAM file</option> + <option value="per_sam_file" selected="True">Per BAM/SAM file</option><!-- <option value="per_read_group">Per Read Group</option> --><validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator></param> diff -r 125d735c689ee60ad9bd9601c7a22738ba3523de -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 tools/samtools/sam_merge.xml --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -4,11 +4,12 @@ <requirement type="package">picard</requirement></requirements><command> -java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 +java -Xmx2G -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MergeSamFiles.jar MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT O=$output1 I=$input1 I=$input2 #for $i in $inputs I=${i.input} #end for 2> $outlog + || echo "Error running Picard MergeSamFiles" >&2 </command><inputs><param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam" @@ -16,10 +17,10 @@ <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file" truevalue="true" falsevalue="false" checked="yes" help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" /> - <param name="input1" label="First file" type="data" format="bam" /> - <param name="input2" label="with file" type="data" format="bam" help="Need to add more files? Use controls below." /> + <param name="input1" label="First file" type="data" format="bam,sam" /> + <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." /><repeat name="inputs" title="Input Files"> - <param name="input" label="Add file" type="data" format="bam" /> + <param name="input" label="Add file" type="data" format="bam,sam" /></repeat></inputs><outputs> @@ -36,7 +37,7 @@ <param name="input1" value="sam_merge_in1.bam" ftype="bam" /><param name="input2" value="sam_merge_in2.bam" ftype="bam" /><output name="output1" file="sam_merge_out1.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="10"/> + <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/></test><test><param name="title" value="test2" /> @@ -45,7 +46,7 @@ <param name="input2" value="sam_merge_in2.bam" ftype="bam" /><param name="input" value="sam_merge_in3.bam" ftype="bam" /><output name="output1" file="sam_merge_out2.bam" ftype="bam" /> - <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="10"/> + <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/></test></tests><help> https://bitbucket.org/galaxy/galaxy-central/changeset/89893520cb6d/ changeset: 89893520cb6d user: natefoo date: 2011-10-27 20:04:57 summary: Fixes for stuff lost in a merge somewhere. affected #: 1 file diff -r ab8fb6d1f56d6677ccd9dbfa137acf6efbc4d245 -r 89893520cb6d18d1371d2dbf816a83b1d7ae2631 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -107,6 +107,14 @@ try: path = elem.get( "file" ) tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) + if guid is not None: + # Tool was installed from a Galaxy tool shed. + tool.tool_shed = elem.find( "tool_shed" ).text + tool.repository_name = elem.find( "repository_name" ).text + tool.repository_owner = elem.find( "repository_owner" ).text + tool.changeset_revision = elem.find( "changeset_revision" ).text + tool.old_id = elem.find( "id" ).text + tool.version = elem.find( "version" ).text if self.app.config.get_bool( 'enable_tool_tags', False ): tag_names = elem.get( "tags", "" ).split( "," ) for tag_name in tag_names: @@ -367,9 +375,7 @@ # legacy basic mode - provide compatible defaults self.attributes['split_size'] = 20 self.attributes['split_mode'] = 'number_of_parts' - - - + class Tool: """ Represents a computational tool that can be executed through Galaxy. @@ -390,6 +396,13 @@ # easily ensure that parameter dependencies like index files or # tool_data_table_conf.xml entries exist. self.input_params = [] + # Attributes of tools installed from Galaxy tool sheds. + self.tool_shed = None + self.repository_name = None + self.repository_owner = None + self.changeset_revision = None + self.old_id = None + self.version = None # Parse XML element containing configuration self.parse( root, guid=guid ) self.external_runJob_script = app.config.drmaa_external_runjob_script @@ -411,14 +424,15 @@ raise Exception, "Missing tool 'name'" # Get the UNIQUE id for the tool # TODO: can this be generated automatically? - if guid is not None: + if guid is None: + self.id = root.get( "id" ) + self.version = root.get( "version" ) + else: self.id = guid - else: - self.id = root.get( "id" ) if not self.id: - raise Exception, "Missing tool 'id'" + raise Exception, "Missing tool 'id'" self.version = root.get( "version" ) - if not self.version: + if not self.version: # For backward compatibility, some tools may not have versions yet. self.version = "1.0.0" # Support multi-byte tools @@ -806,6 +820,7 @@ group = Repeat() group.name = elem.get( "name" ) group.title = elem.get( "title" ) + group.help = elem.get( "help", None ) group.inputs = self.parse_input_elem( elem, enctypes, context ) group.default = int( elem.get( "default", 0 ) ) group.min = int( elem.get( "min", 0 ) ) @@ -1571,7 +1586,7 @@ name = conversion_name, config_info = self.app.config ) # Wrap actual input dataset input_values[ input.name ] = \ - DatasetFilenameWrapper( input_values[ input.name ], + DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, tool = self, name = input.name, config_info = self.app.config ) https://bitbucket.org/galaxy/galaxy-central/changeset/638d994c4cc7/ changeset: 638d994c4cc7 user: natefoo date: 2011-10-27 20:14:27 summary: Revert changes to cufflinks/tophat, these can be integrated in a seperate commit. affected #: 2 files diff -r 89893520cb6d18d1371d2dbf816a83b1d7ae2631 -r 638d994c4cc7783248357b3cf7403b00924d0016 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,5 @@ -<tool id="cufflinks" name="Cufflinks" version="0.9.1"> +<tool id="cufflinks" name="Cufflinks" version="0.0.5"> + <!-- Wrapper supports Cufflinks versions v1.0.0-v1.0.3 --><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> @@ -14,27 +15,10 @@ ## Include reference annotation? #if $reference_annotation.use_ref == "Use reference annotation": - #if $reference_annotation.annotationSource.reference_annotation_file == "indexed": - -G "${ filter( lambda x: str( x[0] ) == str( $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - #if $reference_annotation.annotationSource.reference_annotation_file == "attribute": - -G "${ filter( lambda x: str( x[0] ) == str( $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - -G "${reference_annotation.annotationSource.ownFile}" - #end if - #end if + -G $reference_annotation.reference_annotation_file #end if - #if $reference_annotation.use_ref == "Use reference annotation guide": - #if $reference_annotation.annotationSource.reference_annotation_file == "indexed": - -g "${ filter( lambda x: str( x[0] ) == str( $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - #if $reference_annotation.annotationSource.reference_annotation_file == "attribute": - -g "${ filter( lambda x: str( x[0] ) == str( $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - -g "${reference_annotation.annotationSource.ownFile}" - #end if - #end if + -g $reference_annotation.reference_annotation_guide_file #end if ## Set paired-end parameters? @@ -77,44 +61,10 @@ </param><when value="No"></when><when value="Use reference annotation"> - <conditional name="annotationSource"> - <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - <option value="attribute">Use input bam metadata.dbkey attribute</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select genome for gtf annotation"> - <options from_data_table="gtf_index"> - <filter type="sort_by" column="3" /> - <validator type="no_options" message="No indexes are available for the selected input dataset" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> - </when> - </conditional> - </when> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when><when value="Use reference annotation guide"> - <conditional name="annotationSource"> - <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - <option value="attribute">Use input bam metadata.dbkey attribute</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select genome for gtf annotation"> - <options from_data_table="gtf_index"> - <filter type="sort_by" column="3" /> - <validator type="no_options" message="No indexes are available for the selected input dataset" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> - </when> - </conditional> + <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when></conditional><conditional name="bias_correction"> diff -r 89893520cb6d18d1371d2dbf816a83b1d7ae2631 -r 638d994c4cc7783248357b3cf7403b00924d0016 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,8 +1,7 @@ -<tool id="tophat" name="Tophat" version="1.2.1"> +<tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> + <version_command>tophat --version</version_command><requirements> - <requirement type="package">samtools</requirement> - <requirement type="package">bowtie</requirement><requirement type="package">tophat</requirement></requirements><command interpreter="python"> @@ -18,18 +17,14 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - #if $refGenomeSource.genomeSource == "indexed": - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" - #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" - #end if + --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" #end if ## Are reads single-end or paired? --single-paired=$singlePaired.sPaired ## First input file always required. - --input1=$singlePaired.input1 + --input1=$input1 ## Set params based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": @@ -57,15 +52,7 @@ ## Supplying junctions parameters. #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes": - #if $singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "indexed": - -G "${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - #if $singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "attribute": - -G "${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else - -G "${singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.owngtfFile}" - #end if - #end if + -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model #end if #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes": -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs @@ -124,15 +111,7 @@ ## Supplying junctions parameters. #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes": - #if $singlePaired.pParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "indexed": - -G "${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else: - #if $singlePaired.pParams.own_junctions.gene_model_ann.annotationSource.reference_annotation_file == "attribute": - -G "${ filter( lambda x: str( x[0] ) == str( $singlePaired.input1.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() )[0][-1] }" - #else - -G "${singlePaired.sParams.own_junctions.gene_model_ann.annotationSource.owngtfFile}" - #end if - #end if + -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model #end if #if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes": -j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs @@ -166,15 +145,18 @@ #end if </command><inputs> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option><option value="history">Use one from the history</option> - <option value="attribute">Use input fastq metadata.dbkey attribute</option></param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="tophat_indexes" /> + <options from_data_table="tophat_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options></param></when><when value="history"> @@ -187,7 +169,6 @@ <option value="paired">Paired-end</option></param><when value="single"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><conditional name="sParams"><param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."><option value="preSet">Use Defaults</option> @@ -237,16 +218,7 @@ </param><when value="No" /><when value="Yes"> - <conditional name="annotationSource"> - <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - <option value="attribute">Use metadata.bkey attribute from input fastq file</option> - </param> - <when value="history"> - <param name="owngtfFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> - </when> - </conditional> + <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs"> @@ -291,7 +263,7 @@ <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /></when><when value="No" /> - </conditional> + </conditional><param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."><option value="No">No</option><option value="Yes">Yes</option> @@ -300,8 +272,7 @@ </conditional><!-- sParams --></when><!-- single --><when value="paired"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /><param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /><conditional name="pParams"><param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> @@ -352,16 +323,7 @@ </param><when value="No" /><when value="Yes"> - <conditional name="annotationSource"> - <param name="reference_annotation_file" type="select" label="Please select a reference Aonnotation"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - <option value="attribute">Use metadata.bkey attribute from input fastq files</option> - </param> - <when value="history"> - <param name="owngtfFile" type="data" format="gff3, gtf" label="Select a reference annotation file" /> - </when> - </conditional> + <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs"> @@ -425,7 +387,7 @@ ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) - ) + ) </filter><actions><conditional name="refGenomeSource.genomeSource"> @@ -513,46 +475,49 @@ </outputs><tests> - <!-- Test single-end reads with pre-built index and preset parameters --> + <!-- Test base-space single-end reads with pre-built index and preset parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -p 1 /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger + tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger + Rename the files in tmp_dir appropriately --> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="genomeSource" value="indexed" /><param name="index" value="tophat_test" /><param name="sPaired" value="single" /> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /><output name="junctions" file="tophat_out1j.bed" /><output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test> - <!-- Test using test data: paired-end reads, index from history. --> + <!-- Test using base-space test data: paired-end reads, index from history. --><test><!-- TopHat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger + Rename the files in tmp_dir appropriately --> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="genomeSource" value="history" /><param name="ownFile" ftype="fasta" value="tophat_in1.fasta" /><param name="sPaired" value="paired" /> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="mate_inner_distance" value="20" /><param name="pSettingsType" value="preSet" /><output name="junctions" file="tophat_out2j.bed" /><output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test> - <!-- Test single-end reads with user-supplied reference fasta and full parameters --> + <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters --><test><!-- Tophat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger Replace the + with double-dash + Rename the files in tmp_dir appropriately --> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="genomeSource" value="history"/><param name="ownFile" value="tophat_in1.fasta"/><param name="sPaired" value="single"/> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="sSettingsType" value="full"/><param name="library_type" value="FR Unstranded"/><param name="anchor_length" value="8"/> @@ -585,16 +550,17 @@ <output name="junctions" file="tophat_out3j.bed" /><output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" /></test> - <!-- Test paired-end reads with user-supplied reference fasta and full parameters --> + <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search /afs/bx.psu.edu/depot/data/genome/test/tophat/tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger + tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger Replace the + with double-dash + Rename the files in tmp_dir appropriately --> + <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="genomeSource" value="indexed"/><param name="index" value="tophat_test"/><param name="sPaired" value="paired"/> - <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="full"/> @@ -662,7 +628,9 @@ .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 .. _BAM: http://samtools.sourceforge.net/ - + +Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format. + ------- **Tophat settings** @@ -681,7 +649,7 @@ --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one - read with this many bases on each side. This must be at least 3 and the default is 8. + read with this many bases on each side. This must be at least 3 and the default is 8. -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. https://bitbucket.org/galaxy/galaxy-central/changeset/3f0872314937/ changeset: 3f0872314937 user: natefoo date: 2011-10-27 22:36:46 summary: A couple more fixes. affected #: 4 files diff -r 638d994c4cc7783248357b3cf7403b00924d0016 -r 3f08723149377d3f10b53909f97f90edd4babf6e lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -778,7 +778,7 @@ jeha_false_path = None if self.app.config.outputs_to_working_directory: self.output_paths = [] - output_dataset_paths = {} + self.output_dataset_paths = {} for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) dsp = DatasetPath( data.id, data.file_name, false_path ) @@ -908,7 +908,7 @@ else: self.prepare_input_files_cmds = None self.status = task.states.NEW - + def get_job( self ): if self.job_id: return self.sa_session.query( model.Job ).get( self.job_id ) diff -r 638d994c4cc7783248357b3cf7403b00924d0016 -r 3f08723149377d3f10b53909f97f90edd4babf6e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -649,7 +649,7 @@ permitted_actions = get_permitted_actions( filter='DATASET' ) file_path = "/tmp/" engine = None - def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True): + def __init__( self, id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True ): self.id = id self.state = state self.deleted = False diff -r 638d994c4cc7783248357b3cf7403b00924d0016 -r 3f08723149377d3f10b53909f97f90edd4babf6e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -819,7 +819,7 @@ if elem.tag == "repeat": group = Repeat() group.name = elem.get( "name" ) - group.title = elem.get( "title" ) + group.title = elem.get( "title" ) group.help = elem.get( "help", None ) group.inputs = self.parse_input_elem( elem, enctypes, context ) group.default = int( elem.get( "default", 0 ) ) diff -r 638d994c4cc7783248357b3cf7403b00924d0016 -r 3f08723149377d3f10b53909f97f90edd4babf6e universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -586,9 +586,6 @@ # run with the runner defined with default_cluster_job_runner. [galaxy:tool_runners] -binsort = drmaa://-cwd -V -pe threaded 4/ -bwa_wrapper = drmaa://-cwd -V -pe threaded 4/ -unified_genotyper = drmaa://-cwd -V -pe threaded 2/ biomart = local:/// encode_db1 = local:/// hbvar = local:/// https://bitbucket.org/galaxy/galaxy-central/changeset/0dbc8f529441/ changeset: 0dbc8f529441 user: natefoo date: 2011-10-31 21:15:00 summary: Some fixes to actual user code to negate the need for world-writable directories and write external metadata and job stdout/stderr to the job working directory. affected #: 6 files diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -81,6 +81,7 @@ self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root ) self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) ) self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) ) + self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) self.admin_users = kwargs.get( "admin_users", "" ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") @@ -219,14 +220,6 @@ os.makedirs( path ) except Exception, e: raise ConfigurationError( "Unable to create missing directory: %s\n%s" % ( path, e ) ) - if self.drmaa_external_runjob_script: - os.chmod(self.new_file_path, 0777) - os.chmod(self.job_working_directory, 0777) - os.chmod(self.cluster_files_directory, 0777) - else: - os.chmod(self.new_file_path, 0755) - os.chmod(self.job_working_directory, 0755) - os.chmod(self.cluster_files_directory, 0755) # Check that required files exist for path in self.tool_configs: diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -332,6 +332,9 @@ # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) + self.__user_system_pwent = None + self.__galaxy_system_pwent = None + def get_job_runner( self ): return self.tool.job_runner @@ -360,15 +363,15 @@ config files. """ self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner + if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) - if self.app.config.drmaa_external_runjob_script: - os.chmod(self.working_directory , 0777) # Restore parameters from the database job = self.get_job() if job.user is None and job.galaxy_session is None: raise Exception( 'Job %s has no user and no session.' % job.id ) + incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) incoming = self.tool.params_from_strings( incoming, self.app ) # Do any validation that could not be done at job creation @@ -526,6 +529,21 @@ # default post job setup self.sa_session.expunge_all() job = self.get_job() + + if self.app.config.drmaa_external_runjob_script and job.user is not None: + try: + # FIXME: hardcoded path + cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ] + log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) + p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + stdout, stderr = p.communicate() + assert p.returncode == 0 + except: + # TODO: log stdout/stderr + log.exception( '(%s) Failed to change ownership of %s, failing' % ( job.id, self.working_directory ) ) + self.fail( job.info ) + return + # if the job was deleted, don't finish it if job.state == job.states.DELETED: self.cleanup() @@ -698,16 +716,6 @@ # fix permissions for path in [ dp.real_path for dp in self.get_output_fnames() ]: - #change the ownership of the files in file_path directory back to galaxy user - if self.app.config.drmaa_external_runjob_script and self.app.config.external_chown_script: - galaxy_user_name = pwd.getpwuid(os.getuid())[0] - galaxy_group_id = str(pwd.getpwuid(os.getuid())[3]) - p = subprocess.Popen([ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, path,galaxy_user_name,galaxy_group_id], shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - (stdoutdata, stderrdata) = p.communicate() - exitcode = p.returncode - if exitcode != 0: - ## There was an error in the child process - raise RuntimeError("External_chown_script failed (exit code %s) with error %s" % (str(exitcode), stderrdata)) util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) self.sa_session.flush() log.debug( 'job %d ended' % self.job_id ) @@ -718,10 +726,10 @@ try: for fname in self.extra_filenames: os.remove( fname ) + if self.app.config.set_metadata_externally: + self.external_output_metadata.cleanup_external_metadata( self.sa_session ) if self.working_directory is not None and os.path.isdir( self.working_directory ): shutil.rmtree( self.working_directory ) - if self.app.config.set_metadata_externally: - self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) except: @@ -892,6 +900,33 @@ else: return 'anonymous@unknown' + def change_ownership_for_run( self ): + job = self.get_job() + if self.app.config.external_chown_script and job.user is not None: + try: + # FIXME: hardcoded path + cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, self.user_system_pwent[0], str( self.user_system_pwent[3] ) ] + log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) + p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + stdout, stderr = p.communicate() + assert p.returncode == 0 + except: + log.exception( '(%s) Failed to change ownership of %s, making world-writable instead' % ( job.id, self.working_directory ) ) + os.chmod( self.working_directory, 0777 ) + + @property + def user_system_pwent( self ): + if self.__user_system_pwent is None: + job = self.get_job() + self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] ) + return self.__user_system_pwent + + @property + def galaxy_system_pwent( self ): + if self.__galaxy_system_pwent is None: + self.__galaxy_system_pwent = pwd.getpwuid(os.getuid()) + return self.__galaxy_system_pwent + class TaskWrapper(JobWrapper): """ Extension of JobWrapper intended for running tasks. diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -31,7 +31,7 @@ commands += "; cd %s; " % os.path.abspath( os.getcwd() ) commands += job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = self.app.config.new_file_path, + tmp_dir = job_wrapper.working_directory, dataset_files_path = self.app.model.Dataset.file_path, output_fnames = job_wrapper.get_output_fnames(), set_extension = False, diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -53,8 +53,6 @@ cd %s %s %s -%s -%s """ def __lineno__(): """Returns the current line number in our program.""" @@ -168,8 +166,8 @@ job_wrapper.change_state( model.Job.states.QUEUED ) # define job attributes - ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) - efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) + ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) jt = self.ds.createJobTemplate() jt.remoteCommand = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job_wrapper.get_id_tag()) jt.outputPath = ":%s" % ofile @@ -191,12 +189,7 @@ else: export_tmp = '' - if self.external_runJob_script == None: - script = drm_template % (job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ),export_tmp, command_line,'','') - else: - touchcmd = 'touch ' + os.path.abspath( job_wrapper.working_directory ) + '/just_in_cases.txt' - chmodcmd = 'chmod -Rf a+rwx ' + os.path.abspath( job_wrapper.working_directory ) + '/*' - script = drm_template % (job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ), export_tmp, command_line, touchcmd,chmodcmd) + script = drm_template % ( job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ), export_tmp, command_line ) fh = file( jt.remoteCommand, "w" ) fh.write( script ) @@ -219,9 +212,10 @@ if self.external_runJob_script is None: job_id = self.ds.runJob(jt) else: - userid = self.get_qsub_user(job_wrapper) + job_wrapper.change_ownership_for_run() + log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) filename = self.store_jobtemplate(job_wrapper, jt) - job_id = self.external_runjob(filename, userid) + job_id = self.external_runjob(filename, job_wrapper.user_system_pwent[2]).strip() log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) ) # store runner information for tracking if Galaxy restarts @@ -315,23 +309,23 @@ efile = drm_job_state.efile job_file = drm_job_state.job_file # collect the output - # JED - HACK to wait for the files to appear + # wait for the files to appear which_try = 0 - while which_try < 60: + while which_try < (self.app.config.retry_job_output_collection + 1): try: ofh = file(ofile, "r") efh = file(efile, "r") stdout = ofh.read( 32768 ) stderr = efh.read( 32768 ) - which_try = 60 + which_try = (self.app.config.retry_job_output_collection + 1) except: - if which_try == 60: + if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' - log.debug(stderr) + log.debug( stderr ) else: - which_try += 1 time.sleep(1) + which_try += 1 try: drm_job_state.job_wrapper.finish( stdout, stderr ) @@ -389,9 +383,9 @@ def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" drm_job_state = DRMAAJobState() - drm_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.id) - drm_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id) - drm_job_state.job_file = "%s/database/pbs/galaxy_%s.sh" % (os.getcwd(), job.id) + drm_job_state.ofile = "%s.drmout" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + drm_job_state.efile = "%s.drmerr" % os.path.join(os.getcwd(), job_wrapper.working_directory, job_wrapper.get_id_tag()) + drm_job_state.job_file = "%s/galaxy_%s.sh" % (self.app.config.cluster_files_directory, job.id) drm_job_state.job_id = str( job.job_runner_external_id ) drm_job_state.runner_url = job_wrapper.get_job_runner() job_wrapper.command_line = job.command_line @@ -407,30 +401,22 @@ drm_job_state.running = False self.monitor_queue.put( drm_job_state ) - def get_qsub_user(self, job_wrapper): - """ Returns the UserID (or Username) that should be used to execute the job. """ - #TODO: - #add some logic to decide on an SGE user for the given job. - job_user_name = job_wrapper.user.split('@') - self.job_user_uid = getpwnam(job_user_name[0]) - log.debug (" (%s) is the uid being passed to the DRM queu\n" % ( self.job_user_uid[2]) ) - return self.job_user_uid[2] - def store_jobtemplate(self, job_wrapper, jt): """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string. Path is hard-coded, but it's no worse than other path in this module. Uses Galaxy's JobID, so file is expected to be unique.""" - filename = "%s/database/pbs/%s.jt_json" % (os.getcwd(), job_wrapper.get_id_tag()) + filename = "%s/%s.jt_json" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) data = {} for attr in DRMAA_jobTemplate_attributes: try: data[attr] = getattr(jt, attr) except: pass - s = json.dumps(data); + s = json.dumps(data) f = open(filename,'w') f.write(s) f.close() + log.debug( '(%s) Job script for external submission is: %s' % ( job_wrapper.job_id, filename ) ) return filename def external_runjob(self, jobtemplate_filename, username): diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 scripts/external_chown_script.py --- a/scripts/external_chown_script.py +++ b/scripts/external_chown_script.py @@ -15,8 +15,6 @@ pkg_resources.require("drmaa") import drmaa - - def validate_paramters(): if len(sys.argv)<4: sys.stderr.write("usage: %s path user_name gid\n" % sys.argv[0]) @@ -26,16 +24,12 @@ galaxy_user_name = sys.argv[2] gid = sys.argv[3] - - return path, galaxy_user_name, gid def main(): path, galaxy_user_name, gid = validate_paramters() - os.system('chown %s %s' %(galaxy_user_name, path)) - os.system('chgrp %s %s' %(gid, path)) - - + os.system('chown -Rh %s %s' %(galaxy_user_name, path)) + os.system('chgrp -Rh %s %s' %(gid, path)) if __name__ == "__main__": main() diff -r 3f08723149377d3f10b53909f97f90edd4babf6e -r 0dbc8f529441cb79585c520a062ea01940714814 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -519,6 +519,13 @@ # Galaxy server after the job completes. #outputs_to_working_directory = False +# If your network filesystem's caching prevents the Galaxy server from seeing +# the job's stdout and stderr files when it completes, you can retry reading +# these files. The job runner will retry the number of times specified below, +# waiting 1 second between tries. For NFS, you may want to try the -noac mount +# option (Linux) or -actimeo=0 (Solaris). +#retry_job_output_collection = 0 + # Number of concurrent jobs to run (local job runner) #local_job_queue_workers = 5 @@ -556,9 +563,9 @@ # Also the # Defaults requiretty # in /etc/sudoers must be commented out -#drmaa_external_runjob_script = /opt/galaxy/scripts/drmaa_external_runner.py -#drmaa_external_killjob_script = /opt/galaxy/scripts/drmaa_external_killer.py -#external_chown_script = /opt/galaxy/scripts/external_chown_script.py +#drmaa_external_runjob_script = scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = scripts/drmaa_external_killer.py +#external_chown_script = scripts/external_chown_script.py #important if running as actual user since enviromental variables are not passed #will supercede an other definition of TMPDIR if using drmaa https://bitbucket.org/galaxy/galaxy-central/changeset/ce2673f8f212/ changeset: ce2673f8f212 user: natefoo date: 2011-11-02 14:18:47 summary: Run as user: Don't overwrite stdout/stderr on finish. affected #: 1 file diff -r 0dbc8f529441cb79585c520a062ea01940714814 -r ce2673f8f2122c4d2cf455f35b9bdc42b540a373 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -536,7 +536,7 @@ cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ] log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) - stdout, stderr = p.communicate() + p.wait() assert p.returncode == 0 except: # TODO: log stdout/stderr https://bitbucket.org/galaxy/galaxy-central/changeset/574db4e4ea45/ changeset: 574db4e4ea45 user: natefoo date: 2011-11-02 15:49:17 summary: Fix a merge error in model/__init__.py affected #: 1 file diff -r ce2673f8f2122c4d2cf455f35b9bdc42b540a373 -r 574db4e4ea45c90d02c89110879ace47085a1ac4 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -480,23 +480,6 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval - def get_api_value( self, view='collection', value_mapper = None ): - if value_mapper is None: - value_mapper = {} - rval = {} - try: - visible_keys = self.__getattribute__( 'api_' + view + '_visible_keys' ) - except AttributeError: - raise Exception( 'Unknown API view: %s' % view ) - for key in visible_keys: - try: - rval[key] = self.__getattribute__( key ) - if key in value_mapper: - rval[key] = value_mapper.get( key )( rval[key] ) - except AttributeError: - rval[key] = None - return rval - class HistoryUserShareAssociation( object ): def __init__( self ): self.history = None @@ -1149,28 +1132,6 @@ return hda_name def get_access_roles( self, trans ): return self.dataset.get_access_roles( trans ) - def get_api_value( self, view='collection' ): - # Since this class is a proxy to rather complex attributes we want to - # display in other objects, we can't use the simpler method used by - # other model classes. - hda = self - rval = dict( name = hda.name, - extension = hda.extension, - deleted = hda.deleted, - visible = hda.visible, - state = hda.state, - file_size = int( hda.get_size() ), - genome_build = hda.dbkey, - misc_info = hda.info, - misc_blurb = hda.blurb ) - for name, spec in hda.metadata.spec.items(): - val = hda.metadata.get( name ) - if isinstance( val, MetadataFile ): - val = val.file_name - elif isinstance( val, list ): - val = ', '.join( [str(v) for v in val] ) - rval['metadata_' + name] = val - return rval def quota_amount( self, user ): """ If the user has multiple instances of this dataset, it will not affect their disk usage statistic. https://bitbucket.org/galaxy/galaxy-central/changeset/9ec467c9268d/ changeset: 9ec467c9268d user: natefoo date: 2011-11-02 17:08:40 summary: Run as user: Removed a few more chmods that shouldn't be necessary with everything happening in the job working directory. affected #: 4 files diff -r 574db4e4ea45c90d02c89110879ace47085a1ac4 -r 9ec467c9268d58d995b81cec3499804d572d5430 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -365,20 +365,17 @@ def stop_job( self, job ): """Attempts to delete a job from the DRM queue""" - if self.external_killJob_script is None: - try: - self.ds.control( job.job_runner_external_id, drmaa.JobControlAction.TERMINATE ) - log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) - except drmaa.InvalidJobException: - log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.id, job.job_runner_external_id ) ) - except Exception, e: - log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) - else: - try: - subprocess.Popen(['/usr/bin/sudo','-E', self.external_killJob_script, str(job.job_runner_external_id), str(self.job_user_uid[2])],shell=False) - log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) - except Exception, e: - log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) + try: + if self.external_killJob_script is None: + self.ds.control( job.job_runner_external_id, drmaa.JobControlAction.TERMINATE ) + else: + # FIXME: hardcoded path + subprocess.Popen( [ '/usr/bin/sudo', '-E', self.external_killJob_script, str( job.job_runner_external_id ), str( self.job_user_uid[2] ) ], shell=False ) + log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) + except drmaa.InvalidJobException: + log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.id, job.job_runner_external_id ) ) + except Exception, e: + log.debug( "(%s/%s) User killed running job, but error encountered removing from DRM queue: %s" % ( job.id, job.job_runner_external_id, e ) ) def recover( self, job, job_wrapper ): """Recovers jobs stuck in the queued/running state when Galaxy started""" diff -r 574db4e4ea45c90d02c89110879ace47085a1ac4 -r 9ec467c9268d58d995b81cec3499804d572d5430 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -653,7 +653,6 @@ # Create directory if it does not exist if not os.path.exists( dir ): os.makedirs( dir ) - os.chmod(dir, 0777) # Return filename inside hashed directory return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) else: @@ -1795,8 +1794,6 @@ # File Exists is okay, otherwise reraise if e.errno != errno.EEXIST: raise - - os.chmod(path, 0777) # Return filename inside hashed directory return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) diff -r 574db4e4ea45c90d02c89110879ace47085a1ac4 -r 9ec467c9268d58d995b81cec3499804d572d5430 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1707,10 +1707,10 @@ fd, config_filename = tempfile.mkstemp( dir=directory ) os.close( fd ) f = open( config_filename, "wt" ) - os.chmod(config_filename, 0777) f.write( fill_template( template_text, context=param_dict ) ) f.close() - os.chmod(config_filename, 0777) + # For running jobs as the actual user, ensure the config file is globally readable + os.chmod( config_filename, 0644 ) param_dict[name] = config_filename config_filenames.append( config_filename ) return config_filenames @@ -1843,25 +1843,23 @@ """ for name, hda in output.items(): temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) - #try: - if os.path.exists(temp_file_path) and len( os.listdir( temp_file_path ) ) > 0: - store_file_path = os.path.join( - os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), + try: + if len( os.listdir( temp_file_path ) ) > 0: + store_file_path = os.path.join( + os.path.join( self.app.config.file_path, *directory_hash_id( hda.dataset.id ) ), "dataset_%d_files" % hda.dataset.id ) - os.mkdir(store_file_path) - os.system('mv %s/* %s/' %(temp_file_path ,store_file_path)) - # Fix permissions - if self.external_runJob_script == None: + shutil.move( temp_file_path, store_file_path ) + # Fix permissions for basedir, dirs, files in os.walk( store_file_path ): util.umask_fix_perms( basedir, self.app.config.umask, 0777, self.app.config.gid ) for file in files: path = os.path.join( basedir, file ) # Ignore symlinks if os.path.islink( path ): - continue + continue util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) - #except: - #continue + except: + continue def collect_child_datasets( self, output): """ diff -r 574db4e4ea45c90d02c89110879ace47085a1ac4 -r 9ec467c9268d58d995b81cec3499804d572d5430 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -282,12 +282,9 @@ trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) # Create an empty file immediately - self.external_runJob_script = trans.app.config.drmaa_external_runjob_script - if self.external_runJob_script == None: - open( data.file_name, "w" ).close() - # Fix permissions - util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666) - log.debug('.DAT file name = %s\n' %(data.file_name)) + open( data.file_name, "w" ).close() + # Fix permissions + util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666) # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. https://bitbucket.org/galaxy/galaxy-central/changeset/f701f2805fff/ changeset: f701f2805fff user: natefoo date: 2011-11-04 00:03:55 summary: Fix for splitting with outputs_to_working_directory = True, also rename a dict and method in jobs to refer to hda instead of dataset to avoid (my own) confusion. affected #: 4 files diff -r 9ec467c9268d58d995b81cec3499804d572d5430 -r f701f2805fff88e6ad94d40b00dd8dc72f0ef48f lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -327,7 +327,7 @@ self.working_directory = \ os.path.join( self.app.config.job_working_directory, str( self.job_id ) ) self.output_paths = None - self.output_dataset_paths = None + self.output_hdas_and_paths = None self.tool_provided_job_metadata = None # Wrapper holding the info required to restore and clean up from files used for setting metadata externally self.external_output_metadata = metadata.JobExternalOutputMetadataWrapper( job ) @@ -764,10 +764,10 @@ self.compute_outputs() return self.output_paths - def get_output_datasets_and_fnames( self ): - if self.output_dataset_paths is None: + def get_output_hdas_and_fnames( self ): + if self.output_hdas_and_paths is None: self.compute_outputs() - return self.output_dataset_paths + return self.output_hdas_and_paths def compute_outputs( self ) : class DatasetPath( object ): @@ -786,18 +786,18 @@ jeha_false_path = None if self.app.config.outputs_to_working_directory: self.output_paths = [] - self.output_dataset_paths = {} - for name, data in [ ( da.name, da.dataset.dataset ) for da in job.output_datasets + job.output_library_datasets ]: - false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % data.id ) ) - dsp = DatasetPath( data.id, data.file_name, false_path ) + self.output_hdas_and_paths = {} + for name, hda in [ ( da.name, da.dataset ) for da in job.output_datasets + job.output_library_datasets ]: + false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % hda.dataset.id ) ) + dsp = DatasetPath( hda.dataset.id, hda.dataset.file_name, false_path ) self.output_paths.append( dsp ) - self.output_dataset_paths[name] = data, dsp + self.output_hdas_and_paths[name] = hda, dsp if jeha: jeha_false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % jeha.dataset.id ) ) else: - results = [ (da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name )) for da in job.output_datasets + job.output_library_datasets ] + results = [ ( da.name, da.dataset, DatasetPath( da.dataset.dataset.id, da.dataset.file_name ) ) for da in job.output_datasets + job.output_library_datasets ] self.output_paths = [t[2] for t in results] - self.output_dataset_paths = dict([(t[0], t[1:]) for t in results]) + self.output_hdas_and_paths = dict([(t[0], t[1:]) for t in results]) if jeha: dsp = DatasetPath( jeha.dataset.id, jeha.dataset.file_name, jeha_false_path ) self.output_paths.append( dsp ) diff -r 9ec467c9268d58d995b81cec3499804d572d5430 -r f701f2805fff88e6ad94d40b00dd8dc72f0ef48f lib/galaxy/jobs/splitters/basic.py --- a/lib/galaxy/jobs/splitters/basic.py +++ b/lib/galaxy/jobs/splitters/basic.py @@ -6,7 +6,7 @@ def set_basic_defaults(job_wrapper): parent_job = job_wrapper.get_job() job_wrapper.tool.parallelism.attributes['split_inputs'] = parent_job.input_datasets[0].name - job_wrapper.tool.parallelism.attributes['merge_outputs'] = job_wrapper.get_output_datasets_and_fnames().keys()[0] + job_wrapper.tool.parallelism.attributes['merge_outputs'] = job_wrapper.get_output_hdas_and_fnames().keys()[0] def do_split (job_wrapper): if len(job_wrapper.get_input_fnames()) > 1 or len(job_wrapper.get_output_fnames()) > 1: diff -r 9ec467c9268d58d995b81cec3499804d572d5430 -r f701f2805fff88e6ad94d40b00dd8dc72f0ef48f lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -33,7 +33,6 @@ subdir_index[0] = subdir_index[0] + 1 if not os.path.exists(dir): os.makedirs(dir) - os.chmod(dir,0777) task_dirs.append(dir) return dir @@ -118,7 +117,7 @@ working_directory = job_wrapper.working_directory task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] # TODO: Output datasets can be very complex. This doesn't handle metadata files - outputs = job_wrapper.get_output_datasets_and_fnames() + outputs = job_wrapper.get_output_hdas_and_fnames() pickone_done = [] task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')] for output in outputs: @@ -143,6 +142,7 @@ raise Exception(log_error) except Exception, e: stdout = 'Error merging files'; + log.exception( stdout ) stderr = str(e) https://bitbucket.org/galaxy/galaxy-central/changeset/89ade2dfb20a/ changeset: 89ade2dfb20a user: ichorny date: 2011-11-04 18:47:40 summary: Fix for killing jobs using external jobKillin script affected #: 1 file diff -r f701f2805fff88e6ad94d40b00dd8dc72f0ef48f -r 89ade2dfb20a1167305df832c6d5eaabf671c2a0 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -113,6 +113,7 @@ self.external_runJob_script = app.config.drmaa_external_runjob_script self.external_killJob_script = app.config.drmaa_external_killjob_script self.TMPDIR = app.config.TMPDIR + self.userid = [] def get_native_spec( self, url ): """Get any native DRM arguments specified by the site configuration""" @@ -215,6 +216,7 @@ job_wrapper.change_ownership_for_run() log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) filename = self.store_jobtemplate(job_wrapper, jt) + self.userid = job_wrapper.user_system_pwent[2] job_id = self.external_runjob(filename, job_wrapper.user_system_pwent[2]).strip() log.info("(%s) queued as %s" % ( galaxy_id_tag, job_id ) ) @@ -370,7 +372,7 @@ self.ds.control( job.job_runner_external_id, drmaa.JobControlAction.TERMINATE ) else: # FIXME: hardcoded path - subprocess.Popen( [ '/usr/bin/sudo', '-E', self.external_killJob_script, str( job.job_runner_external_id ), str( self.job_user_uid[2] ) ], shell=False ) + subprocess.Popen( [ '/usr/bin/sudo', '-E', self.external_killJob_script, str( job.job_runner_external_id ), str( self.userid ) ], shell=False ) log.debug( "(%s/%s) Removed from DRM queue at user's request" % ( job.id, job.job_runner_external_id ) ) except drmaa.InvalidJobException: log.debug( "(%s/%s) User killed running job, but it was already dead" % ( job.id, job.job_runner_external_id ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/42c8a6cfaa5b/ changeset: 42c8a6cfaa5b user: ichorny date: 2011-11-05 00:59:30 summary: made a change to sniff.py to copyfile instead of move. Move fails when running as actual user affected #: 1 file diff -r 89ade2dfb20a1167305df832c6d5eaabf671c2a0 -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -95,7 +95,7 @@ fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() if in_place: - shutil.move( temp_name, fname ) + shutil.copyfile( temp_name, fname ) # Return number of lines in file. return ( i + 1, None ) else: https://bitbucket.org/galaxy/galaxy-central/changeset/f05722e66a8a/ changeset: f05722e66a8a user: natefoo date: 2011-11-07 20:17:43 summary: merge. affected #: 64 files diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -71,6 +71,7 @@ self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) ) + self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -462,15 +462,16 @@ dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' - def split( input_files, subdir_generator_function, split_params): + def split( cls, input_datasets, subdir_generator_function, split_params): """ Split the input files by line. """ if split_params is None: return - if len(input_files) > 1: + if len(input_datasets) > 1: raise Exception("Text file splitting does not support multiple files") + input_files = [ds.file_name for ds in input_datasets] lines_per_file = None chunk_size = None @@ -534,7 +535,7 @@ part_file.close() raise f.close() - split = staticmethod(split) + split = classmethod(split) class LineCount( Text ): """ diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/datatypes/display_applications/parameters.py --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -94,13 +94,11 @@ if target_ext and not converted_dataset: if isinstance( data, DisplayDataValueWrapper ): data = data.value - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - trans.sa_session.flush() - assoc.dataset = new_data + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) trans.sa_session.add( assoc ) trans.sa_session.flush() elif converted_dataset and converted_dataset.state == converted_dataset.states.ERROR: diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -192,27 +192,9 @@ Tabular.__init__( self, **kwd ) self.column_names = [] - def make_html_table( self, dataset, skipchars=[] ): - """ - Create HTML table, used for displaying peek - """ - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_mime(self): """Returns the mime type of the datatype""" diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -219,33 +219,9 @@ os.write(fd, '%s\n' % '\t'.join(tmp) ) os.close(fd) return open(temp_name) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append('<tr>') - for i in range( 1, dataset.metadata.columns+1 ): - if i == dataset.metadata.chromCol: - out.append( '<th>%s.Chrom</th>' % i ) - elif i == dataset.metadata.startCol: - out.append( '<th>%s.Start</th>' % i ) - elif i == dataset.metadata.endCol: - out.append( '<th>%s.End</th>' % i ) - elif dataset.metadata.strandCol and i == dataset.metadata.strandCol: - out.append( '<th>%s.Strand</th>' % i ) - elif dataset.metadata.nameCol and i == dataset.metadata.nameCol: - out.append( '<th>%s.Name</th>' % i ) - else: - out.append( '<th>%s</th>' % i ) - out.append('</tr>') - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % str( exc ) - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'endCol':'End', 'strandCol':'Strand', 'nameCol':'Name'} ) def ucsc_links( self, dataset, type, app, base_url ): """ Generate links to UCSC genome browser sites based on the dbkey @@ -617,21 +593,9 @@ except: pass Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_estimated_display_viewport( self, dataset ): """ Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 @@ -1081,7 +1045,8 @@ link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) return ret_val - def make_html_table( self, dataset ): + def display_peek( self, dataset ): + """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) def set_meta( self, dataset, overwrite = True, **kwd ): max_data_lines = None diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -164,64 +164,69 @@ dataset.metadata.comment_lines = comment_lines dataset.metadata.column_types = column_types dataset.metadata.columns = len( column_types ) - def make_html_table( self, dataset, skipchars=[] ): + def make_html_table( self, dataset, **kwargs ): """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] try: - out.append( '<tr>' ) - # Generate column header - for i in range( 1, dataset.metadata.columns+1 ): - out.append( '<th>%s</th>' % str( i ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + out.append( self.make_html_peek_header( dataset, **kwargs ) ) + out.append( self.make_html_peek_rows( dataset, **kwargs ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc: out = "Can't create peek %s" % str( exc ) return out - def make_html_peek_rows( self, dataset, skipchars=[] ): - out = [""] - comments = [] - if not dataset.peek: - dataset.set_peek() - data = dataset.peek - lines = data.splitlines() - for line in lines: - line = line.rstrip( '\r\n' ) - if not line: - continue - comment = False - for skipchar in skipchars: - if line.startswith( skipchar ): - comments.append( line ) - comment = True - break - if comment: - continue - elems = line.split( '\t' ) - if len( elems ) != dataset.metadata.columns: - # We may have an invalid comment line or invalid data - comments.append( line ) - comment = True - continue - while len( comments ) > 0: # Keep comments - try: - out.append( '<tr><td colspan="100%">' ) - except: - out.append( '<tr><td>' ) - out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) + def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ): + out = [] + try: + column_headers = [None] * dataset.metadata.columns + + # fill in empty headers with data from column_names + for i in range( min( dataset.metadata.columns, len( column_names ) ) ): + if column_headers[i] is None and column_names[i] is not None: + column_headers[i] = column_names[i] + + # fill in empty headers from ColumnParameters set in the metadata + for name, spec in dataset.metadata.spec.items(): + if isinstance( spec.param, metadata.ColumnParameter ): + try: + i = int( getattr( dataset.metadata, name ) ) - 1 + except: + i = -1 + if 0 <= i < dataset.metadata.columns and column_headers[i] is None: + column_headers[i] = column_parameter_alias.get(name, name) + out.append( '<tr>' ) - for elem in elems: # valid data - elem = escape( elem ) - out.append( '<td>%s</td>' % elem ) + for i, header in enumerate( column_headers ): + out.append( '<th>' ) + if header is None: + out.append( column_number_format % str( i + 1 ) ) + else: + out.append( '%s.%s' % ( str( i + 1 ), escape( header ) ) ) + out.append( '</th>' ) out.append( '</tr>' ) - # Peek may consist only of comments - while len( comments ) > 0: - try: - out.append( '<tr><td colspan="100%">' ) - except: - out.append( '<tr><td>' ) - out.append( '%s</td></tr>' % escape( comments.pop(0) ) ) + except Exception, exc: + raise Exception, "Can't create peek header %s" % str( exc ) + return "".join( out ) + def make_html_peek_rows( self, dataset, skipchars=[], **kwargs ): + out = [] + try: + if not dataset.peek: + dataset.set_peek() + for line in dataset.peek.splitlines(): + if line.startswith( tuple( skipchars ) ): + out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) ) + elif line: + elems = line.split( '\t' ) + # we may have an invalid comment line or invalid data + if len( elems ) != dataset.metadata.columns: + out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) ) + else: + out.append( '<tr>' ) + for elem in elems: + out.append( '<td>%s</td>' % escape( elem ) ) + out.append( '</tr>' ) + except Exception, exc: + raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) @@ -252,26 +257,9 @@ 'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily', 'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies' ] - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - # This data type requires at least 24 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) class Sam( Tabular ): file_ext = 'sam' @@ -281,25 +269,10 @@ self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT' ] - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - # This data type requires at least 11 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) + def sniff( self, filename ): """ Determines whether the file is in SAM format @@ -393,29 +366,9 @@ def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append('<tr>') - for i in range( 1, dataset.metadata.columns+1 ): - if i == dataset.metadata.chromCol: - out.append( '<th>%s.Chrom</th>' % i ) - elif i == dataset.metadata.startCol: - out.append( '<th>%s.Start</th>' % i ) - elif i == dataset.metadata.baseCol: - out.append( '<th>%s.Base</th>' % i ) - else: - out.append( '<th>%s</th>' % i ) - out.append('</tr>') - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % str( exc ) - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'baseCol':'Base'} ) def repair_methods( self, dataset ): """Return options for removing errors along with a description""" @@ -481,21 +434,9 @@ def sniff( self, filename ): headers = get_headers( filename, '\n', count=1 ) return headers[0][0].startswith("##fileformat=VCF") + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out - def get_track_type( self ): - return "FeatureTrack", {"data": "tabix", "index": "summary_tree"} + return "VcfTrack", {"data": "tabix", "index": "summary_tree"} diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -43,13 +43,11 @@ data = converted_dataset else: #run converter here - assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, metadata_safe = False ) new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] new_data.hid = data.hid new_data.name = data.name trans.sa_session.add( new_data ) - trans.sa_session.flush() - assoc.dataset = new_data + assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = data, file_type = target_ext, dataset = new_data, metadata_safe = False ) trans.sa_session.add( assoc ) trans.sa_session.flush() data = new_data diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -135,10 +135,137 @@ { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ 'index' : attrs[ 'index' ] } ) return filters + +# +# -- Base mixins and providers -- +# + +class FilterableMixin: + def get_filters( self ): + """ Returns a dataset's filters. """ + + # is_ functions taken from Tabular.set_meta + def is_int( column_text ): + try: + int( column_text ) + return True + except: + return False + def is_float( column_text ): + try: + float( column_text ) + return True + except: + if column_text.strip().lower() == 'na': + return True #na is special cased to be a float + return False + + # + # Get filters. + # TODOs: + # (a) might be useful to move this into each datatype's set_meta method; + # (b) could look at first N lines to ensure GTF attribute types are consistent. + # + filters = [] + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + if isinstance( self.original_dataset.datatype, Gff ): + # Can filter by score and GTF attributes. + filters = [ { 'name': 'Score', + 'type': 'int', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c6' } ] + filter_col += 1 + if isinstance( self.original_dataset.datatype, Gtf ): + # Create filters based on dataset metadata. + for name, a_type in self.original_dataset.metadata.attribute_types.items(): + if a_type in [ 'int', 'float' ]: + filters.append( + { 'name': name, + 'type': a_type, + 'index': filter_col, + 'tool_id': 'gff_filter_by_attribute', + 'tool_exp_name': name } ) + filter_col += 1 + + ''' + # Old code: use first line in dataset to find attributes. + for i, line in enumerate( open(self.original_dataset.file_name) ): + if not line.startswith('#'): + # Look at first line for attributes and types. + attributes = parse_gff_attributes( line.split('\t')[8] ) + for attr, value in attributes.items(): + # Get attribute type. + if is_int( value ): + attr_type = 'int' + elif is_float( value ): + attr_type = 'float' + else: + attr_type = 'str' + # Add to filters. + if attr_type is not 'str': + filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) + filter_col += 1 + break + ''' + elif isinstance( self.original_dataset.datatype, Bed ): + # Can filter by score column only. + filters = [ { 'name': 'Score', + 'type': 'int', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c5' + } ] + + return filters + + +class TabixDataProvider( FilterableMixin, TracksDataProvider ): + """ + Tabix index data provider for the Galaxy track browser. + """ + + col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } + + def get_iterator( self, chrom, start, end ): + start, end = int(start), int(end) + if end >= (2<<29): + end = (2<<29 - 1) # Tabix-enforced maximum + + bgzip_fname = self.dependencies['bgzip'].file_name + + # if os.path.getsize(self.converted_dataset.file_name) == 0: + # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." } + tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + + # If chrom is not found in indexes, try removing the first three + # characters (e.g. 'chr') and see if that works. This enables the + # provider to handle chrome names defined as chrXXX and as XXX. + chrom = str(chrom) + if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): + chrom = chrom[3:] + + return tabix.fetch(reference=chrom, start=start, end=end) + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() + +# +# -- BED data providers -- +# class BedDataProvider( TracksDataProvider ): """ - Abstract class that processes BED data from text format to payload format. + Abstract class that processes BED data from native format to payload format. Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ @@ -220,7 +347,168 @@ for line in iterator: out.write( "%s\n" % line ) out.close() - + +class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + +class RawBedDataProvider( BedDataProvider ): + """ + Provide data from BED file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + feature = line.split() + feature_chrom = feature[0] + feature_start = int( feature[1] ) + feature_end = int( feature[2] ) + if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ): + continue + yield line + return line_filter_iter() + +# +# -- VCF data providers -- +# + +class VcfDataProvider( TracksDataProvider ): + """ + Abstract class that processes VCF data from native format to payload format. + + Payload format: TODO + """ + + col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } + + + def get_iterator( self, chrom, start, end ): + raise "Unimplemented Method" + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Returns a dict with the following attributes: + data - a list of variants with the format + [<guid>, <start>, <end>, <name>, cigar, seq] + + message - error/informative message + """ + rval = [] + message = None + + def get_mapping( ref, alt ): + """ + Returns ( offset, new_seq, cigar ) tuple that defines mapping of + alt to ref. Cigar format is an array of [ op_index, length ] pairs + where op_index is the 0-based index into the string "MIDNSHP=X" + """ + + cig_ops = "MIDNSHP=X" + + ref_len = len( ref ) + alt_len = len( alt ) + + # Substitutions? + if ref_len == alt_len: + return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ] + + # Deletions? + alt_in_ref_index = ref.find( alt ) + if alt_in_ref_index != -1: + return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ] + + # Insertions? + ref_in_alt_index = alt.find( ref ) + if ref_in_alt_index != -1: + return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] + + # Pack data. + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + + feature = line.split() + start = int( feature[1] ) - 1 + ref = feature[3] + alts = feature[4] + + # HACK? alts == '.' --> monomorphism. + if alts == '.': + alts = ref + + # Pack variants. + for alt in alts.split(","): + offset, new_seq, cigar = get_mapping( ref, alt ) + start += offset + end = start + len( new_seq ) + + # Pack line. + payload = [ hash( line ), + start, + end, + # ID: + feature[2], + cigar, + # TODO? VCF does not have strand, so default to positive. + "+", + new_seq, + float( feature[5] ) ] + rval.append(payload) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() + +class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): + """ + Provides data from a VCF file indexed via tabix. + """ + pass + +class RawVcfDataProvider( VcfDataProvider ): + """ + Provide data from VCF file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + if line.startswith("#"): + continue + variant = line.split() + variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ] + variant_start = int( variant_start ) + longest_alt = -1 + for alt in alts: + if len( alt ) > longest_alt: + longest_alt = len( alt ) + variant_end = variant_start + abs( len( ref ) - longest_alt ) + if variant_chrom != chrom or variant_start > int( end ) or variant_end < int( start ): + continue + yield line + return line_filter_iter() + class SummaryTreeDataProvider( TracksDataProvider ): """ Summary tree data provider for the Galaxy track browser. @@ -323,11 +611,11 @@ data - a list of reads with the format [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] where <read_1> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] + [<start>, <end>, <cigar>, <strand>, ?<read_seq>?] and <read_2> has the format - [<start>, <end>, <cigar>, ?<read_seq>?] + [<start>, <end>, <cigar>, <strand>, ?<read_seq>?] For single-end reads, read has format: - [<guid>, <start>, <end>, <name>, cigar, seq] + [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>] NOTE: read end and sequence data are not valid for reads outside of requested region and should not be used. @@ -355,17 +643,34 @@ else: return None + # Decode strand from read flag. + def decode_strand( read_flag, mask ): + strand_flag = ( read_flag & mask == 0 ) + if strand_flag: + return "+" + else: + return "-" + # Encode reads as list of lists. results = [] paired_pending = {} + unmapped = 0 for count, read in enumerate( data ): if count < start_val: continue - if count-start_val >= max_vals: + if ( count - start_val - unmapped ) >= max_vals: message = ERROR_MAX_VALS % ( max_vals, "reads" ) break + + # If not mapped, skip read. + is_mapped = ( read.flag & 0x0004 == 0 ) + if not is_mapped: + unmapped += 1 + continue + qname = read.qname seq = read.seq + strand = decode_strand( read.flag, 0x0010 ) if read.cigar is not None: read_len = sum( [cig[1] for cig in read.cigar] ) # Use cigar to determine length else: @@ -378,14 +683,15 @@ pair['start'], read.pos + read_len, qname, - [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], - [ read.pos, read.pos + read_len, read.cigar, seq ] + [ pair['start'], pair['end'], pair['cigar'], pair['strand'], pair['seq'] ], + [ read.pos, read.pos + read_len, read.cigar, strand, seq ] ] ) del paired_pending[qname] else: - paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar } + paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, + 'rlen': read_len, 'strand': strand, 'cigar': read.cigar } else: - results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] ) + results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, strand, read.seq] ) # Take care of reads whose mates are out of range. # TODO: count paired reads when adhering to max_vals? @@ -397,14 +703,14 @@ # Make read_1 start=end so that length is 0 b/c we don't know # read length. r1 = [ read['mate_start'], read['mate_start'] ] - r2 = [ read['start'], read['end'], read['cigar'], read['seq'] ] + r2 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] else: # Mate is after read. read_start = read['start'] # Make read_2 start=end so that length is 0 b/c we don't know # read length. Hence, end of read is start of read_2. read_end = read['mate_start'] - r1 = [ read['start'], read['end'], read['cigar'], read['seq'] ] + r1 = [ read['start'], read['end'], read['cigar'], read['strand'], read['seq'] ] r2 = [ read['mate_start'], read['mate_start'] ] results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] ) @@ -485,118 +791,7 @@ else: f = open( self.original_dataset.file_name ) return f, BigWigFile(file=f) - -class FilterableMixin: - def get_filters( self ): - """ Returns a dataset's filters. """ - - # is_ functions taken from Tabular.set_meta - def is_int( column_text ): - try: - int( column_text ) - return True - except: - return False - def is_float( column_text ): - try: - float( column_text ) - return True - except: - if column_text.strip().lower() == 'na': - return True #na is special cased to be a float - return False - - # - # Get filters. - # TODOs: - # (a) might be useful to move this into each datatype's set_meta method; - # (b) could look at first N lines to ensure GTF attribute types are consistent. - # - filters = [] - # HACK: first 8 fields are for drawing, so start filter column index at 9. - filter_col = 8 - if isinstance( self.original_dataset.datatype, Gff ): - # Can filter by score and GTF attributes. - filters = [ { 'name': 'Score', - 'type': 'int', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c6' } ] - filter_col += 1 - if isinstance( self.original_dataset.datatype, Gtf ): - # Create filters based on dataset metadata. - for name, a_type in self.original_dataset.metadata.attribute_types.items(): - if a_type in [ 'int', 'float' ]: - filters.append( - { 'name': name, - 'type': a_type, - 'index': filter_col, - 'tool_id': 'gff_filter_by_attribute', - 'tool_exp_name': name } ) - filter_col += 1 - - ''' - # Old code: use first line in dataset to find attributes. - for i, line in enumerate( open(self.original_dataset.file_name) ): - if not line.startswith('#'): - # Look at first line for attributes and types. - attributes = parse_gff_attributes( line.split('\t')[8] ) - for attr, value in attributes.items(): - # Get attribute type. - if is_int( value ): - attr_type = 'int' - elif is_float( value ): - attr_type = 'float' - else: - attr_type = 'str' - # Add to filters. - if attr_type is not 'str': - filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) - filter_col += 1 - break - ''' - elif isinstance( self.original_dataset.datatype, Bed ): - # Can filter by score column only. - filters = [ { 'name': 'Score', - 'type': 'int', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c5' - } ] - - return filters - -class TabixDataProvider( FilterableMixin, TracksDataProvider ): - """ - Tabix index data provider for the Galaxy track browser. - """ - - col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - - def get_iterator( self, chrom, start, end ): - start, end = int(start), int(end) - if end >= (2<<29): - end = (2<<29 - 1) # Tabix-enforced maximum - - bgzip_fname = self.dependencies['bgzip'].file_name - - # if os.path.getsize(self.converted_dataset.file_name) == 0: - # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." } - tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) - - # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): - chrom = chrom[3:] - - return tabix.fetch(reference=chrom, start=start, end=end) - - def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): - iterator = self.get_iterator( chrom, start, end ) - return self.process_data( iterator, start_val, max_vals, **kwargs ) - + class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): """ Interval index files used only for GFF files. @@ -658,41 +853,6 @@ results.append( payload ) return { 'data': results, 'message': message } - -class VcfDataProvider( TabixDataProvider ): - """ - VCF data provider for the Galaxy track browser. - - Payload format: - [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score ] - """ - - col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - - def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): - rval = [] - message = None - - for count, line in enumerate( iterator ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( "max_vals", "features" ) - break - - feature = line.split() - payload = [ hash(line), int(feature[1])-1, int(feature[1]), - # ID: - feature[2], - # reference base(s): - feature[3], - # alternative base(s) - feature[4], - # phred quality score - float( feature[5] )] - rval.append(payload) - - return { 'data': rval, 'message': message } class GFFDataProvider( TracksDataProvider ): """ @@ -724,40 +884,16 @@ offset += feature.raw_size return { 'data': results, 'message': message } - -class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): - """ - Provides data from a BED file indexed via tabix. - """ - pass - -class RawBedDataProvider( BedDataProvider ): - """ - Provide data from BED file. - - NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. - """ - - def get_iterator( self, chrom, start, end ): - def line_filter_iter(): - for line in open( self.original_dataset.file_name ): - feature = line.split() - feature_chrom, feature_start, feature_end = feature[ 0:3 ] - if feature_chrom != chrom or feature_start > end or feature_end < start: - continue - yield line - return line_filter_iter() - + # -# Helper methods. +# -- Helper methods. -- # # Mapping from dataset type name to a class that can fetch data from a file of that # type. First key is converted dataset type; if result is another dict, second key # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { - "tabix": { Vcf: VcfDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, + "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -410,7 +410,8 @@ columns = [ NameColumn( "Name", key="name", - attach_popup=True ), + link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ), + attach_popup=False ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), RevisionColumn( "Revision" ), @@ -426,17 +427,14 @@ key="free-text-search", visible=False, filterable="standard" ) ) - operations = [ grids.GridOperation( "Get updates", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] standard_filters = [] default_filter = dict( deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .filter( self.model_class.table.c.deleted == False ) class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): @@ -678,11 +676,88 @@ return quota, params @web.expose @web.require_admin - def browse_repositories( self, trans, **kwd ): + def browse_tool_shed_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, kwd[ 'id' ] ) + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + tool_dicts = [] + workflow_dicts = [] + for root, dirs, files in os.walk( repo_files_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories. + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files. + files.remove( 'hgrc' ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + tool = trans.app.toolbox.load_tool( full_path ) + if tool is not None: + tool_config = os.path.join( root, name ) + # Handle tool.requirements. + tool_requirements = [] + for tr in tool.requirements: + name=tr.name + type=tr.type + if type == 'fabfile': + version = None + fabfile = tr.fabfile + method = tr.method + else: + version = tr.version + fabfile = None + method = None + requirement_dict = dict( name=name, + type=type, + version=version, + fabfile=fabfile, + method=method ) + tool_requirements.append( requirement_dict ) + tool_dict = dict( id=tool.id, + old_id=tool.old_id, + name=tool.name, + version=tool.version, + description=tool.description, + requirements=tool_requirements, + tool_config=tool_config ) + tool_dicts.append( tool_dict ) + except Exception, e: + # The file is not a Galaxy tool config. + pass + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + full_path = os.path.abspath( os.path.join( root, name ) ) + # Convert workflow data from json + fp = open( full_path, 'rb' ) + workflow_text = fp.read() + fp.close() + workflow_dict = from_json_string( workflow_text ) + if workflow_dict[ 'a_galaxy_workflow' ] == 'true': + workflow_dicts.append( dict( full_path=full_path, workflow_dict=workflow_dict ) ) + except Exception, e: + # The file is not a Galaxy workflow. + pass + return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', + repository=repository, + tool_dicts=tool_dicts, + workflow_dicts=workflow_dicts, + message=message, + status=status ) + @web.expose + @web.require_admin + def browse_tool_shed_repositories( self, trans, **kwd ): if 'operation' in kwd: - operation = kwd.pop('operation').lower() - if operation == "get updates": - return self.check_for_updates( trans, **kwd ) + operation = kwd.pop( 'operation' ).lower() + if operation == "manage_repository": + return self.manage_tool_shed_repository( trans, **kwd ) # Render the list view return self.repository_list_grid( trans, **kwd ) @web.expose @@ -725,7 +800,7 @@ message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose ' message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the ' message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_..." ' - message += 'target=_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' + message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the ' message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.' return trans.show_error_message( message ) message = kwd.get( 'message', '' ) @@ -766,12 +841,9 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: - # Add a new record to the tool_shed_repository table. - tool_shed_repository = self.__create_tool_shed_repository( trans, - name, - description, - changeset_revision, - repository_clone_url ) + # Add a new record to the tool_shed_repository table if one doesn't + # already exist. If one exists but is marked deleted, undelete it. + self.__create_or_undelete_tool_shed_repository( trans, name, description, changeset_revision, repository_clone_url ) # Update the cloned repository to changeset_revision. repo_files_dir = os.path.join( clone_dir, name ) log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) @@ -853,10 +925,35 @@ status=status ) @web.expose @web.require_admin + def manage_tool_shed_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_id = params.get( 'id', None ) + repository = get_repository( trans, repository_id ) + description = util.restore_text( params.get( 'description', repository.description ) ) + if params.get( 'edit_repository_button', False ): + if description != repository.description: + repository.description = description + trans.sa_session.add( repository ) + trans.sa_session.flush() + message = "The repository information has been updated." + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + if relative_install_dir: + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + else: + repo_files_dir = 'unknown' + return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', + repository=repository, + description=description, + repo_files_dir=repo_files_dir, + message=message, + status=status ) + @web.expose + @web.require_admin def check_for_updates( self, trans, **kwd ): params = util.Params( kwd ) - repository_id = params.get( 'id', None ) - repository = get_repository( trans, repository_id ) + repository = get_repository( trans, kwd[ 'id' ] ) galaxy_url = trans.request.host # Send a request to the relevant tool shed to see if there are any updates. # TODO: support https in the following url. @@ -875,26 +972,16 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) latest_changeset_revision = params.get( 'latest_changeset_revision', None ) + repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision: if changeset_revision == latest_changeset_revision: message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name else: - repository = get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ) current_working_dir = os.getcwd() - # Get the directory where the repository is cloned. - cleaned_tool_shed_url = self.__clean_tool_shed_url( tool_shed_url ) - partial_cloned_dir = '%s/repos/%s/%s/%s' % ( cleaned_tool_shed_url, owner, name, changeset_revision ) - # Get the relative tool installation paths from each of the shed tool configs. - shed_tool_confs = trans.app.toolbox.shed_tool_confs - relative_cloned_dir = None - # The shed_tool_confs dictionary contains shed_conf_filename : tool_path pairs. - for shed_conf_filename, tool_path in shed_tool_confs.items(): - relative_cloned_dir = os.path.join( tool_path, partial_cloned_dir ) - if os.path.isdir( relative_cloned_dir ): - break - if relative_cloned_dir: + relative_install_dir = self.__get_relative_install_dir( trans, repository ) + if relative_install_dir: # Update the cloned repository to changeset_revision. - repo_files_dir = os.path.join( relative_cloned_dir, name ) + repo_files_dir = os.path.join( relative_install_dir, name ) log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \ ( name, changeset_revision, latest_changeset_revision ) ) cmd = 'hg pull' @@ -938,9 +1025,44 @@ message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name status = 'error' return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repositories', + action='manage_tool_shed_repository', + id=trans.security.encode_id( repository.id ), message=message, status=status ) ) + @web.expose + @web.require_admin + def impersonate( self, trans, email=None, **kwd ): + if not trans.app.config.allow_user_impersonation: + return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." ) + message = '' + status = 'done' + emails = None + if email is not None: + user = trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first() + if user: + trans.set_user( user ) + message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % ( email, url_for( controller='root' ) ) + emails = [] + else: + message = 'Invalid user selected' + status = 'error' + if emails is None: + emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ] + return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status ) + + def __get_relative_install_dir( self, trans, repository ): + # Get the directory where the repository is install. + tool_shed = self.__clean_tool_shed_url( repository.tool_shed ) + partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.changeset_revision ) + # Get the relative tool installation paths from each of the shed tool configs. + shed_tool_confs = trans.app.toolbox.shed_tool_confs + relative_install_dir = None + # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs. + for shed_conf_filename, tool_path in shed_tool_confs.items(): + relative_install_dir = os.path.join( tool_path, partial_install_dir ) + if os.path.isdir( relative_install_dir ): + break + return relative_install_dir def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): # Inspect each tool to see if any have input parameters that are dynamically # generated select lists that require entries in the tool_data_table_conf.xml file. @@ -1055,17 +1177,26 @@ # We have an invalid .xml file, so not a tool config. log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) return sample_files, repository_tools_tups - def __create_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ): + def __create_or_undelete_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ): tmp_url = self.__clean_repository_clone_url( repository_clone_url ) tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) owner = self.__get_repository_owner( tmp_url ) - tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed, - name=name, - description=description, - owner=owner, - changeset_revision=changeset_revision ) - trans.sa_session.add( tool_shed_repository ) - trans.sa_session.flush() + flush_needed = False + tool_shed_repository = get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ) + if tool_shed_repository: + if tool_shed_repository.deleted: + tool_shed_repository.deleted = False + flush_needed = True + else: + tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed, + name=name, + description=description, + owner=owner, + changeset_revision=changeset_revision ) + flush_needed = True + if flush_needed: + trans.sa_session.add( tool_shed_repository ) + trans.sa_session.flush() def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): # Add an entry in the shed_tool_conf file. An entry looks something like: # <section name="Filter and Sort" id="filter"> @@ -1194,3 +1325,11 @@ trans.model.ToolShedRepository.table.c.owner == owner, trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ .first() +def get_repository_by_shed_name_owner_changeset_revision( trans, tool_shed, name, owner, changeset_revision ): + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( and_( trans.model.ToolShedRepository.table.c.tool_shed == tool_shed, + trans.model.ToolShedRepository.table.c.name == name, + trans.model.ToolShedRepository.table.c.owner == owner, + trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + .first() + diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -465,10 +465,14 @@ data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None - if isinstance( dataset.datatype, Bed ): + elif isinstance( dataset.datatype, Bed ): data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None + elif isinstance( dataset.datatype, Vcf ): + data = RawVcfDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'tabix' + data[ 'extra_info' ] = None return data @web.json @@ -586,7 +590,7 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - result = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) + result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result @@ -840,6 +844,43 @@ # Set input datasets for tool. If running on region, extract and use subset # when possible. # + + def set_param_value( param_dict, param_name, param_value ): + """ + Set new parameter value in a parameter dictionary. + """ + + # Recursive function to set param value. + def set_value( param_dict, group_name, group_index, param_name, param_value ): + if group_name in param_dict: + param_dict[ group_name ][ group_index ][ param_name ] = param_value + return True + elif param_name in param_dict: + param_dict[ param_name ] = param_value + return True + else: + # Recursive search. + return_val = False + for name, value in param_dict.items(): + if isinstance( value, dict ): + return_val = set_value( value, group_name, group_index, param_name, param_value) + if return_val: + return return_val + return False + + # Parse parameter name if necessary. + if param_name.find( "|" ) == -1: + # Non-grouping parameter. + group_name = group_index = None + else: + # Grouping parameter. + group, param_name = param_name.split( "|" ) + index = group.rfind( "_" ) + group_name = group[ :index ] + group_index = int( group[ index + 1: ] ) + + return set_value( param_dict, group_name, group_index, param_name, param_value ) + for jida in original_job.input_datasets: input_dataset = jida.dataset if input_dataset is None: #optional dataset and dataset wasn't selected @@ -875,10 +916,20 @@ new_dataset.set_size() new_dataset.info = "Data subset for trackster" new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) + + # Set metadata. + if trans.app.config.set_metadata_externally: + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset } ) + else: + message = 'Attributes updated' + new_dataset.set_meta() + new_dataset.datatype.after_setting_metadata( new_dataset ) + trans.sa_session.flush() - + # Add dataset to tool's parameters. - tool_params[ jida.name ] = new_dataset + if not set_param_value( tool_params, jida.name, new_dataset ): + return to_json_string( { "error" : True, "message" : "error setting parameter %s" % jida.name } ) # # Execute tool and handle outputs. diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1095,8 +1095,8 @@ @web.expose def import_workflow( self, trans, **kwd ): """ - Import a workflow by reading an url, uploading a file, or receiving the textual - representation of a workflow. + Import a workflow by reading an url, uploading a file, opening and reading the contents + of a local file, or receiving the textual representation of a workflow via http. """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) @@ -1104,6 +1104,8 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) + # The following parameters will have values only if the workflow + # id being imported from a Galaxy tool shed repository. tool_shed_url = kwd.get( 'tool_shed_url', '' ) repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) # The workflow_name parameter is in the request only if the import originated @@ -1111,6 +1113,15 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) + # The following parameters will have a value only if the import originated + # from a tool shed repository installed locally. + local_file = kwd.get( 'local_file', '' ) + repository_id = kwd.get( 'repository_id', '' ) + if local_file and not import_button: + workflow_file = open( local_file, 'rb' ) + workflow_text = workflow_file.read() + workflow_file.close() + import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. workflow_url = 'http://%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ @@ -1118,7 +1129,6 @@ response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() - workflow_text = workflow_text import_button = True if import_button: workflow_data = None @@ -1131,6 +1141,7 @@ message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( url, str( e ) ) status = 'error' elif workflow_text: + # This case occurs when the workflow_text was sent via http from the tool shed. workflow_data = workflow_text else: # Load workflow from browsed file. @@ -1170,7 +1181,7 @@ message += "Imported, but this workflow contains cycles. " status = "error" else: - message += "Workflow '%s' imported successfully. " % workflow.name + message += "Workflow <b>%s</b> imported successfully. " % workflow.name if missing_tool_tups: if trans.user_is_admin(): # A required tool is not available in the local Galaxy instance. @@ -1182,30 +1193,49 @@ # the Galaxy panels displayed whenever in Galaxy. message += "The workflow requires the following tools that are not available in this Galaxy instance." message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/><br/>" - for tool_shed_name, tool_shed_url in trans.app.tool_shed_registry.tool_sheds.items(): - if tool_shed_url.endswith( '/' ): - tool_shed_url = tool_shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, trans.request.host ) + for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp ) for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] url += '&tool_id=%s' % missing_tool_id - message += '<a href="%s">%s</a><br/>' % ( url, tool_shed_name ) + message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' - return trans.response.send_redirect( web.url_for( controller='admin', - action='index', - webapp='galaxy', - message=message, - status=status ) ) + if local_file or tool_shed_url: + # Another Galaxy panels Hack: The request did not originate from the Galaxy + # workflow view, so we don't need to render the Galaxy panels. + return trans.response.send_redirect( web.url_for( controller='admin', + action='center', + webapp='galaxy', + message=message, + status=status ) ) + else: + # Another Galaxy panels hack: The request originated from the Galaxy + # workflow view, so we need to render the Galaxy panels. + return trans.response.send_redirect( web.url_for( controller='admin', + action='index', + webapp='galaxy', + message=message, + status=status ) ) else: # TODO: Figure out what to do here... pass if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. - message = "This workflow has been successfully imported into your local Galaxy instance." + message = "Workflow <b>%s</b> imported successfully." % workflow.name # TODO: support https in the following url. url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) return trans.response.send_redirect( url ) + elif local_file: + # The workflow was read from a file included with an installed tool shed repository. + message = "Workflow <b>%s</b> imported successfully." % workflow.name + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tool_shed_repository', + id=repository_id, + message=message, + status=status ) ) return self.list( trans ) return trans.fill_template( "workflow/import.mako", url=url, @@ -1277,7 +1307,16 @@ for job_id in job_ids: assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" job = jobs_by_id[ job_id ] - tool = trans.app.toolbox.tools_by_id[ job.tool_id ] + try: + tool = trans.app.toolbox.tools_by_id[ job.tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id + # attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if job.tool_id == available_tool.old_id: + tool = available_tool + break param_values = job.get_param_values( trans.app ) associations = cleanup_param_values( tool.inputs, param_values ) # Doing it this way breaks dynamic parameters, backed out temporarily. @@ -1444,7 +1483,16 @@ # Execute module job = None if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id + # attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break input_values = step.state.inputs # Connect up def callback( input, value, prefixed_name, prefixed_label ): @@ -1480,10 +1528,10 @@ trans.sa_session.add( workflow_invocation ) invocations.append({'outputs': outputs, 'new_history': new_history}) - trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) + trans.sa_session.flush() + return trans.fill_template( "workflow/run_complete.mako", + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -361,8 +361,9 @@ workflow_text = fp.read() fp.close() exported_workflow_dict = from_json_string( workflow_text ) - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) + if exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + # Update the list of metadata dictionaries for workflows in metadata_dict. + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) else: diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -339,12 +339,6 @@ workflow.has_errors = True # Stick this in the step temporarily. step.temp_input_connections = step_dict[ 'input_connections' ] - # Unpack and add post-job actions. - post_job_actions = step_dict.get( 'post_job_actions', {} ) - for name, pja_dict in post_job_actions.items(): - pja = PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) steps.append( step ) steps_by_external_id[ step_dict[ 'id' ] ] = step # Second pass to deal with connections between steps. diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/jquery.scrollTo.js --- a/static/scripts/jquery.scrollTo.js +++ /dev/null @@ -1,215 +0,0 @@ -/** - * jQuery.ScrollTo - * Copyright (c) 2007-2009 Ariel Flesler - aflesler(at)gmail(dot)com | http://flesler.blogspot.com - * Dual licensed under MIT and GPL. - * Date: 5/25/2009 - * - * @projectDescription Easy element scrolling using jQuery. - * http://flesler.blogspot.com/2007/10/jqueryscrollto.html - * Works with jQuery +1.2.6. Tested on FF 2/3, IE 6/7/8, Opera 9.5/6, Safari 3, Chrome 1 on WinXP. - * - * @author Ariel Flesler - * @version 1.4.2 - * - * @id jQuery.scrollTo - * @id jQuery.fn.scrollTo - * @param {String, Number, DOMElement, jQuery, Object} target Where to scroll the matched elements. - * The different options for target are: - * - A number position (will be applied to all axes). - * - A string position ('44', '100px', '+=90', etc ) will be applied to all axes - * - A jQuery/DOM element ( logically, child of the element to scroll ) - * - A string selector, that will be relative to the element to scroll ( 'li:eq(2)', etc ) - * - A hash { top:x, left:y }, x and y can be any kind of number/string like above. -* - A percentage of the container's dimension/s, for example: 50% to go to the middle. - * - The string 'max' for go-to-end. - * @param {Number} duration The OVERALL length of the animation, this argument can be the settings object instead. - * @param {Object,Function} settings Optional set of settings or the onAfter callback. - * @option {String} axis Which axis must be scrolled, use 'x', 'y', 'xy' or 'yx'. - * @option {Number} duration The OVERALL length of the animation. - * @option {String} easing The easing method for the animation. - * @option {Boolean} margin If true, the margin of the target element will be deducted from the final position. - * @option {Object, Number} offset Add/deduct from the end position. One number for both axes or { top:x, left:y }. - * @option {Object, Number} over Add/deduct the height/width multiplied by 'over', can be { top:x, left:y } when using both axes. - * @option {Boolean} queue If true, and both axis are given, the 2nd axis will only be animated after the first one ends. - * @option {Function} onAfter Function to be called after the scrolling ends. - * @option {Function} onAfterFirst If queuing is activated, this function will be called after the first scrolling ends. - * @return {jQuery} Returns the same jQuery object, for chaining. - * - * @desc Scroll to a fixed position - * @example $('div').scrollTo( 340 ); - * - * @desc Scroll relatively to the actual position - * @example $('div').scrollTo( '+=340px', { axis:'y' } ); - * - * @dec Scroll using a selector (relative to the scrolled element) - * @example $('div').scrollTo( 'p.paragraph:eq(2)', 500, { easing:'swing', queue:true, axis:'xy' } ); - * - * @ Scroll to a DOM element (same for jQuery object) - * @example var second_child = document.getElementById('container').firstChild.nextSibling; - * $('#container').scrollTo( second_child, { duration:500, axis:'x', onAfter:function(){ - * alert('scrolled!!'); - * }}); - * - * @desc Scroll on both axes, to different values - * @example $('div').scrollTo( { top: 300, left:'+=200' }, { axis:'xy', offset:-20 } ); - */ -;(function( $ ){ - - var $scrollTo = $.scrollTo = function( target, duration, settings ){ - $(window).scrollTo( target, duration, settings ); - }; - - $scrollTo.defaults = { - axis:'xy', - duration: parseFloat($.fn.jquery) >= 1.3 ? 0 : 1 - }; - - // Returns the element that needs to be animated to scroll the window. - // Kept for backwards compatibility (specially for localScroll & serialScroll) - $scrollTo.window = function( scope ){ - return $(window)._scrollable(); - }; - - // Hack, hack, hack :) - // Returns the real elements to scroll (supports window/iframes, documents and regular nodes) - $.fn._scrollable = function(){ - return this.map(function(){ - var elem = this, - isWin = !elem.nodeName || $.inArray( elem.nodeName.toLowerCase(), ['iframe','#document','html','body'] ) != -1; - - if( !isWin ) - return elem; - - var doc = (elem.contentWindow || elem).document || elem.ownerDocument || elem; - - return $.browser.safari || doc.compatMode == 'BackCompat' ? - doc.body : - doc.documentElement; - }); - }; - - $.fn.scrollTo = function( target, duration, settings ){ - if( typeof duration == 'object' ){ - settings = duration; - duration = 0; - } - if( typeof settings == 'function' ) - settings = { onAfter:settings }; - - if( target == 'max' ) - target = 9e9; - - settings = $.extend( {}, $scrollTo.defaults, settings ); - // Speed is still recognized for backwards compatibility - duration = duration || settings.speed || settings.duration; - // Make sure the settings are given right - settings.queue = settings.queue && settings.axis.length > 1; - - if( settings.queue ) - // Let's keep the overall duration - duration /= 2; - settings.offset = both( settings.offset ); - settings.over = both( settings.over ); - - return this._scrollable().each(function(){ - var elem = this, - $elem = $(elem), - targ = target, toff, attr = {}, - win = $elem.is('html,body'); - - switch( typeof targ ){ - // A number will pass the regex - case 'number': - case 'string': - if( /^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(targ) ){ - targ = both( targ ); - // We are done - break; - } - // Relative selector, no break! - targ = $(targ,this); - case 'object': - // DOMElement / jQuery - if( targ.is || targ.style ) - // Get the real position of the target - toff = (targ = $(targ)).offset(); - } - $.each( settings.axis.split(''), function( i, axis ){ - var Pos = axis == 'x' ? 'Left' : 'Top', - pos = Pos.toLowerCase(), - key = 'scroll' + Pos, - old = elem[key], - max = $scrollTo.max(elem, axis); - - if( toff ){// jQuery / DOMElement - attr[key] = toff[pos] + ( win ? 0 : old - $elem.offset()[pos] ); - - // If it's a dom element, reduce the margin - if( settings.margin ){ - attr[key] -= parseInt(targ.css('margin'+Pos)) || 0; - attr[key] -= parseInt(targ.css('border'+Pos+'Width')) || 0; - } - - attr[key] += settings.offset[pos] || 0; - - if( settings.over[pos] ) - // Scroll to a fraction of its width/height - attr[key] += targ[axis=='x'?'width':'height']() * settings.over[pos]; - }else{ - var val = targ[pos]; - // Handle percentage values - attr[key] = val.slice && val.slice(-1) == '%' ? - parseFloat(val) / 100 * max - : val; - } - - // Number or 'number' - if( /^\d+$/.test(attr[key]) ) - // Check the limits - attr[key] = attr[key] <= 0 ? 0 : Math.min( attr[key], max ); - - // Queueing axes - if( !i && settings.queue ){ - // Don't waste time animating, if there's no need. - if( old != attr[key] ) - // Intermediate animation - animate( settings.onAfterFirst ); - // Don't animate this axis again in the next iteration. - delete attr[key]; - } - }); - - animate( settings.onAfter ); - - function animate( callback ){ - $elem.animate( attr, duration, settings.easing, callback && function(){ - callback.call(this, target, settings); - }); - }; - - }).end(); - }; - - // Max scrolling position, works on quirks mode - // It only fails (not too badly) on IE, quirks mode. - $scrollTo.max = function( elem, axis ){ - var Dim = axis == 'x' ? 'Width' : 'Height', - scroll = 'scroll'+Dim; - - if( !$(elem).is('html,body') ) - return elem[scroll] - $(elem)[Dim.toLowerCase()](); - - var size = 'client' + Dim, - html = elem.ownerDocument.documentElement, - body = elem.ownerDocument.body; - - return Math.max( html[scroll], body[scroll] ) - - Math.min( html[size] , body[size] ); - - }; - - function both( val ){ - return typeof val == 'object' ? val : { top:val, left:val }; - }; - -})( jQuery ); \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/packed/jquery.scrollTo.js --- a/static/scripts/packed/jquery.scrollTo.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(c){var a=c.scrollTo=function(f,e,d){c(window).scrollTo(f,e,d)};a.defaults={axis:"xy",duration:parseFloat(c.fn.jquery)>=1.3?0:1};a.window=function(d){return c(window)._scrollable()};c.fn._scrollable=function(){return this.map(function(){var e=this,d=!e.nodeName||c.inArray(e.nodeName.toLowerCase(),["iframe","#document","html","body"])!=-1;if(!d){return e}var f=(e.contentWindow||e).document||e.ownerDocument||e;return c.browser.safari||f.compatMode=="BackCompat"?f.body:f.documentElement})};c.fn.scrollTo=function(f,e,d){if(typeof e=="object"){d=e;e=0}if(typeof d=="function"){d={onAfter:d}}if(f=="max"){f=9000000000}d=c.extend({},a.defaults,d);e=e||d.speed||d.duration;d.queue=d.queue&&d.axis.length>1;if(d.queue){e/=2}d.offset=b(d.offset);d.over=b(d.over);return this._scrollable().each(function(){var l=this,j=c(l),k=f,i,g={},m=j.is("html,body");switch(typeof k){case"number":case"string":if(/^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(k)){k=b(k);break}k=c(k,this);case"object":if(k.is||k.style){i=(k=c(k)).offset()}}c.each(d.axis.split(""),function(q,r){var s=r=="x"?"Left":"Top",u=s.toLowerCase(),p="scroll"+s,o=l[p],n=a.max(l,r);if(i){g[p]=i[u]+(m?0:o-j.offset()[u]);if(d.margin){g[p]-=parseInt(k.css("margin"+s))||0;g[p]-=parseInt(k.css("border"+s+"Width"))||0}g[p]+=d.offset[u]||0;if(d.over[u]){g[p]+=k[r=="x"?"width":"height"]()*d.over[u]}}else{var t=k[u];g[p]=t.slice&&t.slice(-1)=="%"?parseFloat(t)/100*n:t}if(/^\d+$/.test(g[p])){g[p]=g[p]<=0?0:Math.min(g[p],n)}if(!q&&d.queue){if(o!=g[p]){h(d.onAfterFirst)}delete g[p]}});h(d.onAfter);function h(n){j.animate(g,e,d.easing,n&&function(){n.call(this,f,d)})}}).end()};a.max=function(j,i){var h=i=="x"?"Width":"Height",e="scroll"+h;if(!c(j).is("html,body")){return j[e]-c(j)[h.toLowerCase()]()}var g="client"+h,f=j.ownerDocument.documentElement,d=j.ownerDocument.body;return Math.max(f[e],d[e])-Math.min(f[g],d[g])};function b(d){return typeof d=="object"?d:{top:d,left:d}}})(jQuery); \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(u,t,s){return((u*299)+(t*587)+(s*114))/1000};var e=function(v,u,w,s,r,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,r)-Math.min(u,r))+(Math.max(w,t)-Math.min(w,t))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,I=9,F=20,U=I+2,A=100,K=12000,S=200,D=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",y="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,C=5;function ab(ai,ah){if(!ah){ah=0}var aj=Math.pow(10,ah);return Math.round(ai*aj)/aj}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(J.prototype,T.prototype,c.prototype,{load_data:function(ah,ak,al,ai,aj){if(ai>1){return{data:null}}return T.prototype.load_data.call(this,ah,ak,al,ai,aj)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=al;this.is_overview=false};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var z=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(z.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(ak,ai,ah,aj){z.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!R.id_counter){R.id_counter=0}var al=R.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};q(R.prototype,r.prototype,z.prototype,{update_track_icons:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){z.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,z.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new B(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(am,ai,ao){if(!am||am==="None"){return}var aj=this;if(am==="previous"){aj.load_chroms({low:this.chrom_start_index-x});return}if(am==="next"){aj.load_chroms({low:this.chrom_start_index+x});return}var an=$.grep(aj.chrom_data,function(ap,aq){return ap.chrom===am})[0];if(an===undefined){aj.load_chroms({chrom:am},function(){aj.change_chrom(am,ai,ao)});return}else{if(am!==aj.chrom){aj.chrom=am;aj.chrom_select.val(aj.chrom);aj.max_high=an.len-1;aj.reset();aj.request_redraw(true);for(var al=0,ah=aj.drawables.length;al<ah;al++){var ak=aj.drawables[al];if(ak.init){ak.init()}}}if(ai!==undefined&&ao!==undefined){aj.low=Math.max(ai,0);aj.high=Math.min(ao,aj.max_high)}aj.reset_overview();aj.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){z.prototype.add_drawable.call(this,ah);ah.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;ah.init();this.label_tracks.push(ah)},remove_drawable:function(aj,ai){z.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.drawables),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(D,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(D)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(aj){if(this.overview_drawable){if(this.overview_drawable.dataset_id===aj.dataset_id){return}this.overview_viewport.find(".track").remove()}var ai=aj.copy({content_div:this.overview_viewport}),ah=this;ai.header_div.hide();ai.is_overview=true;ah.overview_drawable=ai;this.overview_drawable.postdraw_actions=function(){ah.overview_highlight.show().height(ah.overview_drawable.content_div.height());ah.overview_viewport.height(ah.overview_drawable.content_div.height()+ah.overview_box.outerHeight());ah.overview_close.show();ah.resize_window()};this.overview_drawable.init();ah.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new R(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new W(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(y+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=ah[this.index];return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(at,aA){this.track=at;this.filters=[];for(var av=0;av<aA.length;av++){var aw=aA[av],aB=aw.name,ah=aw.type,aj=aw.index,az=aw.tool_id,ay=aw.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[av]=new X(aB,aj,az,ay)}else{console.log("ERROR: unsupported filter: ",aB,ah)}}var ak=function(aC,aD,aE){aC.click(function(){var aF=aD.text();max=parseFloat(aE.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aE.slider("option","values")){input_size=2*input_size+1;multi_value=true}aD.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aF).appendTo(aD).focus().select().click(function(aG){aG.stopPropagation()}).blur(function(){$(this).remove();aD.text(aF)}).keyup(function(aK){if(aK.keyCode===27){$(this).trigger("blur")}else{if(aK.keyCode===13){var aI=aE.slider("option","min"),aG=aE.slider("option","max"),aJ=function(aL){return(isNaN(aL)||aL>aG||aL<aI)},aH=$(this).val();if(!multi_value){aH=parseFloat(aH);if(aJ(aH)){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}else{aH=aH.split("-");aH=[parseFloat(aH[0]),parseFloat(aH[1])];if(aJ(aH[0])||aJ(aH[1])){alert("Parameter value must be in the range ["+aI+"-"+aG+"]");return $(this)}}aE.slider((multi_value?"values":"value"),aH)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aC){aC.stopPropagation()}).click(function(aC){aC.stopPropagation()}).bind("dblclick",function(aC){aC.stopPropagation()}).bind("keydown",function(aC){aC.stopPropagation()});var ax=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aF,aH){aH.container=$("<div/>").addClass("filter-row slider-row").appendTo(ax);var aG=$("<div/>").addClass("elt-label").appendTo(aH.container);var aE=$("<span/>").addClass("slider-name").text(aH.name+" ").appendTo(aG);var aD=$("<span/>");var aJ=$("<span/>").addClass("slider-value").appendTo(aG).append("[").append(aD).append("]");var aC=$("<div/>").addClass("slider").appendTo(aH.container);aH.control_element=$("<div/>").attr("id",aH.name+"-filter-control").appendTo(aC);var aI=[0,0];aH.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aL,aM){var aK=aM.values;aD.text(aK[0]+"-"+aK[1]);aH.low=aK[0];aH.high=aK[1];ap.track.request_draw(true,true)},change:function(aK,aL){aH.control_element.slider("option","slide").call(aH.control_element,aK,aL)}});aH.slider=aH.control_element;aH.slider_label=aD;ak(aJ,aD,aH.control_element);$("<div style='clear: both;'/>").appendTo(aH.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(ax);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var ai=this;ao.click(function(){ai.run_on_dataset()})}var ar=$("<div/>").addClass("display-controls").appendTo(this.parent_div),au,an,aq,al={Transparency:function(aC){ap.alpha_filter=aC},Height:function(aC){ap.height_filter=aC}};$.each(al,function(aE,aD){au=$("<div/>").addClass("filter-row").appendTo(ar),an=$("<span/>").addClass("elt-label").text(aE+":").appendTo(au),aq=$("<select/>").attr("name",aE+"_dropdown").css("float","right").appendTo(au);$("<option/>").attr("value",-1).text("== None ==").appendTo(aq);for(var aC=0;aC<ap.filters.length;aC++){$("<option/>").attr("value",aC).text(ap.filters[aC].name).appendTo(aq)}aq.change(function(){$(this).children("option:selected").each(function(){var aF=parseInt($(this).val());al[aE]((aF>=0?ap.filters[aF]:null));ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(au)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var E=function(ah,ai){N.Scaler.call(this,ai);this.filter=ah};E.prototype.gen_val=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(ah,ak,aj,ai,al){this.track=ah;this.index=ak;this.low=ak*S*aj;this.high=(ak+1)*S*aj;this.resolution=aj;this.canvas=$("<div class='track-tile'/>").append(ai);this.data=al;this.stale=false};b.prototype.predisplay_actions=function(){};var l=function(ah,ak,aj,ai,al,am){b.call(this,ah,ak,aj,ai,al);this.max_val=am};q(l.prototype,b.prototype);var Q=function(ah,al,ak,aj,an,ao,am,ai){b.call(this,ah,al,ak,aj,an);this.mode=ao;this.message=am;this.feature_mapper=ai};q(Q.prototype,b.prototype);Q.prototype.predisplay_actions=function(){var ai=this,ah={};if(ai.mode!=="Pack"){return}$(this.canvas).mousemove(function(au){var ao=$(this).offset(),at=au.pageX-ao.left,ar=au.pageY-ao.top,ay=ai.feature_mapper.get_feature_data(at,ar),ap=(ay?ay[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ap||$(this).attr("id")!==ap.toString()){$(this).remove()}});if(ay){var ak=ah[ap];if(!ak){var ap=ay[0],av={name:ay[3],start:ay[1],end:ay[2],strand:ay[4]},an=ai.track.filters_manager.filters,am;for(var aq=0;aq<an.length;aq++){am=an[aq];av[am.name]=ay[am.index]}var ak=$("<div/>").attr("id",ap).addClass("feature-popup"),ax,aw,az=$("<table/>").appendTo(ak),aA;for(ax in av){aw=av[ax];aA=$("<tr/>").appendTo(az);$("<th/>").appendTo(aA).text(ax);$("<td/>").attr("align","left").appendTo(aA).text(typeof(aw)=="number"?ab(aw,2):aw)}ah[ap]=ak}ak.appendTo($(ai.canvas).parent());var al=at+parseInt(ai.canvas.css("left"))+7,aj=ar+parseInt(ai.canvas.css("top"))+7;ak.css("left",al+"px").css("top",aj+"px")}else{if(!au.isPropagationStopped()){au.stopPropagation();$(this).siblings().each(function(){$(this).trigger(au)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var j=function(ak,at,al,ao,au,aj,ai){r.call(this,ak,at,al,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ai?ai:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.id=j.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(ao){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var am=this;this.header_div.dblclick(function(av){av.stopPropagation()});this.settings_icon.click(function(){var ax=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(){am.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aw=function(ay){if((ay.keyCode||ay.which)===27){ax()}else{if((ay.keyCode||ay.which)===13){av()}}};$(window).bind("keypress.check_enter_esc",aw);show_modal("Configure Track",am.config.build_form(),{Cancel:ax,OK:av})});this.overview_icon.click(function(){am.view.set_overview(am)});this.filters_icon.click(function(){am.filters_div.toggle();am.filters_manager.reset_filters()});this.tools_icon.click(function(){am.dynamic_tool_div.toggle();if(am.dynamic_tool_div.is(":visible")){am.set_name(am.name+am.tool_region_and_parameters_str())}else{am.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();am.remove()});if(am.display_modes!==undefined){if(am.mode_div===undefined){am.mode_div=$("<div class='right-float menubutton popup' />").appendTo(am.header_div);var an=(am.config&&am.config.values.mode?am.config.values.mode:am.display_modes[0]);am.mode=an;am.mode_div.text(an);var ah={};for(var ap=0,ar=am.display_modes.length;ap<ar;ap++){var aq=am.display_modes[ap];ah[aq]=function(av){return function(){am.change_mode(av)}}(aq)}make_popupmenu(am.mode_div,ah)}else{am.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){am.icons_div.show()},function(){am.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.update_track_icons()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var O=function(ak,aj){var ai=this,ah=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ak!==undefined?ak:{}));this.filters_available=false;this.filters_visible=false;this.tool=(aj!==undefined&&obj_length(aj)>0?new s(this,aj):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};q(O.prototype,r.prototype,j.prototype,{copy:function(ah){return new this.constructor(this.name,this.view,ah,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},update_track_icons:function(){var ah=this;if(ah.filters_available>0){ah.filters_icon.show()}else{ah.filters_icon.hide()}if(ah.tool){ah.tools_icon.show()}else{ah.tools_icon.hide()}},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof B)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(this.is_overview){aq=this.view.max_low;an=this.view.max_high;am=Math.pow(D,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(D)));av=ak/(view.max_high-view.max_low)}if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);if(aq!==undefined){al.tile_cache.set(at,aq);al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw(false,false,false,al)});return null},show_tile:function(an,ap,aq){var aj=this,ai=an.canvas,am=ai;if(an.message){var ar=$("<div/>"),ao=$("<div/>").addClass("tile-message").text(an.message).css({height:F-1,width:an.canvas.width}).appendTo(ar),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ao),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ao);ar.append(ai);am=ar;al.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()});ah.click(function(){an.stale=true;aj.data_manager.get_more_data(an.low,an.high,aj.mode,an.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(at){at.stopPropagation()})}an.predisplay_actions();var ak=(an.low-(this.is_overview?this.view.max_low:this.view.low))*aq;if(this.left_offset){ak-=this.left_offset}am.css({position:"absolute",top:0,left:ak,height:""});ap.append(am);aj.max_height=Math.max(aj.max_height,am.height());aj.content_div.css("height",aj.max_height+"px");ap.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){j.call(this,"label",ai,ah,false,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{init:function(){this.enabled=true},_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var B=function(ah){j.call(this,"reference",ah,{content_div:ah.top_labeltrack},false,{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(C,this,false);this.tile_cache=new c(v)};q(B.prototype,r.prototype,O.prototype,{init:function(){this.enabled=true},draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar.data===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(al,ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(C,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this;ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(ai){ah.container_div.addClass("line-track");var ak=ai.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=ak.min;ah.prefs.max_value=ak.max;$("#track_"+ah.dataset_id+"_minval").val(ah.prefs.min_value);$("#track_"+ah.dataset_id+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=ak.total_frequency;ah.container_div.find(".yaxislabel").remove();var al=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_minval").text(ab(ah.prefs.min_value,3));var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ah.dataset_id+"_maxval").text(ab(ah.prefs.max_value,3));aj.css({position:"absolute",top:"24px",left:"10px"});aj.prependTo(ah.container_div);al.css({position:"absolute",bottom:"2px",left:"10px"});al.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(this.track,aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,true,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.update_track_icons()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",A,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aD,aH,ar,ak){var aA=this,am=aA._get_tile_bounds(aH,aD),aK=am[0],ai=am[1],ay=ai-aK,aB=Math.ceil(ay*ar),aQ=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"||aA.is_overview){az="no_detail"}else{var aP=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aB+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aM=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aC=aj.getContext("2d");aC.translate(al,U);aM.draw(aC,aB,an);return new l(aA,aH,aD,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aE=0,aG=aw.data.length;aE<aG;aE++){var ao=aw.data[aE];var aF=false;var av;for(var aJ=0,aO=au.length;aJ<aO;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aF=true;break}}if(!aF){aq.push(ao)}}}var aN=(this.filters_manager.alpha_filter?new E(this.filters_manager.alpha_filter):null);var aL=(this.filters_manager.height_filter?new E(this.filters_manager.height_filter):null);var aM=new (this.painter)(aq,aK,ai,this.prefs,az,aN,aL,ak);var an=Math.max(af,aM.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();var aI=null;aj.width=aB+al;aj.height=an;var aC=aj.getContext("2d");aC.fillStyle=this.prefs.block_color;aC.font=aC.canvas.manager.default_font;aC.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aC.translate(al,0);aI=aM.draw(aC,aB,an,ax);aI.translation=-al}return new Q(aA,aH,aD,aj,aw.data,az,aw.message,aI)}});var V=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(V.prototype,r.prototype,O.prototype,e.prototype);var Y=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ak,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=N.ReadPainter;this.update_track_icons()};q(Y.prototype,r.prototype,O.prototype,e.prototype);var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,y){var v=k("class").extend;var q=function(J,B,H,A,G,E){if(E===undefined){E=4}var D=A-B;var C=G-H;var F=Math.floor(Math.sqrt(D*D+C*C)/E);var K=D/F;var I=C/F;var z;for(z=0;z<F;z++,B+=K,H+=I){if(z%2!==0){continue}J.fillRect(B,H,E,1)}};var r=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var e=function(z){this.default_val=(z?z:1)};e.prototype.gen_val=function(z){return this.default_val};var n=function(B,D,z,A,C){this.data=B;this.view_start=D;this.view_end=z;this.prefs=v({},this.default_prefs,A);this.mode=C};n.prototype.default_prefs={};var w=function(B,D,z,A,C){n.call(this,B,D,z,A,C)};w.prototype.default_prefs={show_counts:false};w.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var c=function(z,D,F,G,B){n.call(this,z,D,F,G,B);if(this.prefs.min_value===undefined){var H=Infinity;for(var A=0,C=this.data.length;A<C;A++){H=Math.min(H,this.data[A][1])}this.prefs.min_value=H}if(this.prefs.max_value===undefined){var E=-Infinity;for(var A=0,C=this.data.length;A<C;A++){E=Math.max(E,this.data[A][1])}this.prefs.max_value=E}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(z){this.feature_positions={};this.slot_height=z;this.translation=0};o.prototype.map_feature_data=function(A,C,z,B){if(!this.feature_positions[C]){this.feature_positions[C]=[]}this.feature_positions[C].push({data:A,x_start:z,x_end:B})};o.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var p=function(B,E,z,A,D,F,C){n.call(this,B,E,z,A,D);this.alpha_scaler=(F?F:new e());this.height_scaler=(C?C:new e())};p.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};v(p.prototype,{get_required_height:function(A){var z=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){z=A*y_scale}return z+Math.max(Math.round(y_scale/2),5)},draw:function(L,J,H,G){var R=this.data,E=this.view_start,N=this.view_end;L.save();L.fillStyle=this.prefs.block_color;L.textAlign="right";var I=this.view_end-this.view_start,F=J/I,M=this.get_row_height(),Q=new o(M),C;for(var O=0,P=R.length;O<P;O++){var B=R[O],D=B[0],K=B[1],z=B[2],A=(G&&G[D]!==undefined?G[D]:null);if((K<N&&z>E)&&(this.mode=="Dense"||A!==null)){C=this.draw_element(L,this.mode,B,A,E,N,F,M,J);Q.map_feature_data(B,A,C[0],C[1])}}L.restore();return Q},draw_element:function(F,B,H,D,C,E,G,A,z){console.log("WARNING: Unimplemented function.");return[0,0]}});var d=10,j=3,m=5,x=10,g=1,t=3,f=3,a=9,l=2,h="#ccc";var s=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(s.prototype,p.prototype,{get_row_height:function(){var A=this.mode,z;if(A==="Dense"){z=d}else{if(A==="no_detail"){z=j}else{if(A==="Squish"){z=m}else{z=x}}}return z},draw_element:function(N,E,W,I,P,ah,al,an,z){var T=W[0],aj=W[1],ab=W[2],R=W[3],ac=Math.floor(Math.max(0,(aj-P)*al)),O=Math.ceil(Math.min(z,Math.max(0,(ab-P)*al))),aa=ac,am=O,Z=(E==="Dense"?0:(0+I))*an,M,af,S=null,ap=null,C=this.prefs.block_color,ae=this.prefs.label_color;N.globalAlpha=this.alpha_scaler.gen_val(W);if(E=="Dense"){I=1}if(E==="no_detail"){N.fillStyle=C;N.fillRect(ac,Z+5,O-ac,g)}else{var L=W[4],Y=W[5],ad=W[6],D=W[7];if(Y&&ad){S=Math.floor(Math.max(0,(Y-P)*al));ap=Math.ceil(Math.min(z,Math.max(0,(ad-P)*al)))}var ak,U;if(E==="Squish"||E==="Dense"){ak=1;U=f}else{ak=5;U=a}if(!D){if(W.strand){if(W.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=C}N.fillRect(ac,Z,O-ac,U)}else{var K,V;if(E==="Squish"||E==="Dense"){N.fillStyle=h;K=Z+Math.floor(f/2)+1;V=1}else{if(L){var K=Z;var V=U;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;V=1}}N.fillRect(ac,K,O-ac,V);var F;for(var ai=0,B=D.length;ai<B;ai++){var G=D[ai],A=Math.floor(Math.max(0,(G[0]-P)*al)),X=Math.ceil(Math.min(z,Math.max((G[1]-P)*al)));if(A>X){continue}N.fillStyle=C;N.fillRect(A,Z+(U-ak)/2+1,X-A,ak);if(S!==undefined&&ad>Y&&!(A>ap||X<S)){var ag=Math.max(A,S),J=Math.min(X,ap);N.fillRect(ag,Z+1,J-ag,U);if(D.length==1&&E=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ag+14<J){ag+=2;J-=2}N.fillRect(ag,Z+1,J-ag,U)}}}if(E==="Pack"){N.globalAlpha=1;N.fillStyle="white";var H=this.height_scaler.gen_val(W),Q=Math.ceil(U*H),ao=Math.round((U-Q)/2);if(H!==1){N.fillRect(ac,K+1,O-ac,ao);N.fillRect(ac,K+U-ao+1,O-ac,ao)}}}N.globalAlpha=1;if(E==="Pack"&&aj>P){N.fillStyle=ae;if(P===0&&ac-N.measureText(R).width<0){N.textAlign="left";N.fillText(R,O+l,Z+8);am+=N.measureText(R).width+l}else{N.textAlign="right";N.fillText(R,ac-l,Z+8);aa-=N.measureText(R).width+l}}}N.globalAlpha=1;return[aa,am]}});var b=function(B,E,z,A,D,F,C){p.call(this,B,E,z,A,D,F,C)};v(b.prototype,p.prototype,{draw_element:function(S,N,H,D,V,B,K,T,Q){var H=data[i],J=H[0],R=H[1],C=H[2],M=H[3],F=Math.floor(Math.max(0,(R-V)*K)),I=Math.ceil(Math.min(Q,Math.max(0,(C-V)*K))),E=(N==="Dense"?0:(0+D))*T,z,W,A=null,L=null;if(no_label){S.fillStyle=block_color;S.fillRect(F+left_offset,E+5,I-F,1)}else{var U=H[4],P=H[5],G=H[6];z=9;W=1;S.fillRect(F+left_offset,E,I-F,z);if(N!=="Dense"&&M!==undefined&&R>V){S.fillStyle=label_color;if(V===0&&F-S.measureText(M).width<0){S.textAlign="left";S.fillText(M,I+2+left_offset,E+8)}else{S.textAlign="right";S.fillText(M,F-2+left_offset,E+8)}S.fillStyle=block_color}var O=U+" / "+P;if(R>V&&S.measureText(O).width<(I-F)){S.fillStyle="white";S.textAlign="center";S.fillText(O,left_offset+F+(I-F)/2,E+8);S.fillStyle=block_color}}return[F,I]}});var u=function(C,F,z,B,E,G,D,A){p.call(this,C,F,z,B,E,G,D);this.ref_seq=(A?A.data:null)};u.prototype.default_prefs=v({},p.prototype.default_prefs,{show_insertions:false});v(u.prototype,p.prototype,{get_row_height:function(){var z,A=this.mode;if(A==="Dense"){z=d}else{if(A==="Squish"){z=m}else{z=x;if(this.prefs.show_insertions){z*=2}}}return z},draw_read:function(W,R,N,ab,C,V,K,H,G){W.textAlign="center";var U=this,B=[ab,C],Q=0,X=0,T=0,z=W.canvas.manager.char_width_px;var ag=[];if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){T=Math.round(N/2)}if(!K){K=[[0,H.length]]}for(var O=0,Z=K.length;O<Z;O++){var L=K[O],D="MIDNSHP=X"[L[0]],P=L[1];if(D==="H"||D==="S"){Q-=P}var I=V+Q,af=Math.floor(Math.max(0,(I-ab)*N)),J=Math.floor(Math.max(0,(I+P-ab)*N));if(af===J){J+=1}switch(D){case"H":break;case"S":case"M":case"=":if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(T>0){W.fillStyle=this.prefs.block_color;W.fillRect(af-T,G+1,J-af,9);W.fillStyle=h;for(var ad=0,A=S.length;ad<A;ad++){if(this.prefs.show_differences&&this.ref_seq){var M=this.ref_seq[I-ab+ad];if(!M||M.toLowerCase()===S[ad].toLowerCase()){continue}}if(I+ad>=ab&&I+ad<=C){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae,G+9)}}}else{W.fillStyle=this.prefs.block_color;W.fillRect(af,G+4,J-af,f)}}X+=P;Q+=P;break;case"N":W.fillStyle=h;W.fillRect(af-T,G+5,J-af,1);Q+=P;break;case"D":W.fillStyle="red";W.fillRect(af-T,G+4,J-af,3);Q+=P;break;case"P":break;case"I":var aa=af-T;if(is_overlap([I,I+P],B)){var S=H.slice(X,X+P);if(this.prefs.show_insertions){var F=af-(J-af)/2;if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){W.fillStyle="yellow";W.fillRect(F-T,G-9,J-af,9);ag[ag.length]={type:"triangle",data:[aa,G+4,5]};W.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):S=S.slice(ab-I);break;case (OVERLAP_END):S=S.slice(0,I-C);break;case (CONTAINED_BY):break;case (CONTAINS):S=S.slice(ab-I,I-C);break}for(var ad=0,A=S.length;ad<A;ad++){var ae=Math.floor(Math.max(0,(I+ad-ab)*N));W.fillText(S[ad],ae-(J-af)/2,G)}}else{W.fillStyle="yellow";W.fillRect(F,G+(this.mode!=="Dense"?2:5),J-af,(R!=="Dense"?f:t))}}else{if((R==="Pack"||this.mode==="Auto")&&H!==undefined&&N>z){ag[ag.length]={type:"text",data:[S.length,aa,G+9]}}else{}}}X+=P;break;case"X":X+=P;break}}W.fillStyle="yellow";var ac,E,ah;for(var Y=0;Y<ag.length;Y++){ac=ag[Y];E=ac.type;ah=ac.data;if(E==="text"){W.save();W.font="bold 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U=1;if(U===0&&E-S.measureText(K).width<0){S.textAlign="left";S.fillText(K,G+l-P,D+8)}else{S.textAlign="right";S.fillText(K,E-l-P,D+8)}S.fillStyle=W}return[0,0]}});y.Scaler=e;y.SummaryTreePainter=w;y.LinePainter=c;y.LinkedFeaturePainter=s;y.ReadPainter=u;y.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, 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ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. 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Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var 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ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return 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y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to 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tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/packed/trackster_ui.js --- a/static/scripts/packed/trackster_ui.js +++ b/static/scripts/packed/trackster_ui.js @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -654,6 +654,8 @@ * associated with a view and container. They optionally have a drag handle class. */ var Drawable = function(name, view, container, prefs, drag_handle_class) { + if (!Drawable.id_counter) { Drawable.id_counter = 0; } + this.id = Drawable.id_counter++; this.name = name; this.view = view; this.container = container; @@ -677,7 +679,7 @@ request_draw: function() {}, _draw: function() {}, to_json: function() {}, - update_track_icons: function() {}, + update_icons: function() {}, /** * Set drawable name. */ @@ -804,13 +806,11 @@ DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); // HTML elements. - if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; } - var group_id = DrawableGroup.id_counter++ - this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.container.content_div); + this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); this.header_div.append($("<div/>").addClass(this.drag_handle_class)); this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); - this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div); + this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); // Set up containers/moving for group: register both container_div and content div as container // because both are used as containers (container div to recognize container, content_div to @@ -819,14 +819,14 @@ is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - this.update_track_icons(); + this.update_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { /** * Make popup menu for group. */ - update_track_icons: function() { + update_icons: function() { var group = this; var group_dropdown = {}; @@ -941,7 +941,7 @@ } }; this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls); - this.location_span = $("<span/>").addClass("location").appendTo(this.nav_controls); + this.location_span = $("<span/>").addClass("location").attr('original-title', 'Click to change location').tipsy( { gravity: 'n' } ).appendTo(this.nav_controls); this.location_span.click(function() { view.location_span.hide(); view.chrom_select.hide(); @@ -953,8 +953,11 @@ if (this.vis_id !== undefined) { this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls); } - this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); - this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); + + this.zo_link = $("<a/>").attr("id", "zoom-out").attr("title", "Zoom out").tipsy( {gravity: 'n'} ) + .click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls); + this.zi_link = $("<a/>").attr("id", "zoom-in").attr("title", "Zoom in").tipsy( {gravity: 'n'} ) + .click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); // Get initial set of chroms. this.load_chroms_deferred = this.load_chroms({low: 0}); @@ -1069,11 +1072,10 @@ this.reset(); $(window).trigger("resize"); - this.update_intro_div(); }, /** Add or remove intro div depending on view state. */ update_intro_div: function() { - if (this.num_tracks === 0) { + if (this.drawables.length === 0) { this.intro_div.appendTo(this.viewport_container); } else { @@ -1577,8 +1579,7 @@ // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), - container, - new_track; + container; // If track not in a group, create a group for it and add new track to group. If track // already in group, add track to group. @@ -1595,11 +1596,12 @@ else { container = current_track.container; } - if (current_track instanceof FeatureTrack) { - new_track = new ToolDataFeatureTrack(track_name, view, container, "hda"); - new_track.change_mode(current_track.mode); - container.add_drawable(new_track); - } + + // Create and init new track. + var new_track = new current_track.constructor(track_name, view, container, "hda"); + new_track.init_for_tool_data(); + new_track.change_mode(current_track.mode); + container.add_drawable(new_track); new_track.content_div.text("Starting job."); // Run tool. @@ -2316,7 +2318,6 @@ * ----> ReferenceTrack * ----> FeatureTrack * -------> ReadTrack - * -------> ToolDataFeatureTrack * -------> VcfTrack */ var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { @@ -2330,9 +2331,6 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - - if (!Track.id_counter) { Track.id_counter = 0; } - this.id = Track.id_counter++; // // Create HTML element structure for track. @@ -2476,9 +2474,6 @@ else if (this instanceof ReadTrack) { return "ReadTrack"; } - else if (this instanceof ToolDataFeatureTrack) { - return "ToolDataFeatureTrack"; - } else if (this instanceof VcfTrack) { return "VcfTrack"; } @@ -2538,7 +2533,7 @@ } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; - track.update_track_icons(); + track.update_icons(); } track.content_div.text(DATA_OK); if (track.view.chrom) { @@ -2554,7 +2549,7 @@ } }); - this.update_track_icons(); + this.update_icons(); }, /** * Additional initialization required before drawing track for the first time. @@ -2562,8 +2557,8 @@ predraw_init: function() {} }); -var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) { - Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait); +var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) { + Track.call(this, name, view, container, show_header, prefs); var track = this, view = track.view; @@ -2632,7 +2627,7 @@ /** * Update track's buttons. */ - update_track_icons: function() { + update_icons: function() { var track = this; // @@ -2910,6 +2905,39 @@ region = (chrom !== undefined && low !== undefined && high !== undefined ? chrom + ":" + low + "-" + high : "all"); return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; + }, + /** + * Set up track to receive tool data. + */ + init_for_tool_data: function() { + // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- + // is ready. + this.data_url = raw_data_url; + this.data_query_wait = 1000; + this.dataset_check_url = dataset_state_url; + + /** + * Predraw init sets up postdraw init. + */ + this.predraw_init = function() { + // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. + var track = this; + var post_init = function() { + if (track.data_manager.size() === 0) { + // Track still drawing initial data, so do nothing. + setTimeout(post_init, 300); + } + else { + // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start + // indexing. + track.data_url = default_data_url; + track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; + track.dataset_state_url = converted_datasets_state_url; + $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); + } + }; + post_init(); + } } }); @@ -3261,7 +3289,7 @@ if (!track.filters_available) { track.filters_div.hide(); } - track.update_track_icons(); + track.update_icons(); } } }, @@ -3524,16 +3552,8 @@ } }); -var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); - this.painter = painters.VariantPainter; -}; - -extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); - - -var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); +var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool); this.config = new DrawableConfig( { track: this, @@ -3542,6 +3562,37 @@ { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() }, { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, + { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + ], + saved_values: prefs, + onchange: function() { + this.track.set_name(this.track.prefs.name); + this.track.tile_cache.clear(); + this.track.request_draw(); + } + }); + this.prefs = this.config.values; + + this.painter = painters.ReadPainter; +}; + +extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); + +var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); + + var + block_color = get_random_color(), + reverse_strand_color = get_random_color( [ block_color, "#ffffff" ] ); + this.config = new DrawableConfig( { + track: this, + params: [ + { key: 'name', label: 'Name', type: 'text', default_value: name }, + { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color }, + { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color }, + { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, + { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false }, { key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true }, { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, @@ -3556,48 +3607,10 @@ this.prefs = this.config.values; this.painter = painters.ReadPainter; - this.update_track_icons(); + this.update_icons(); }; extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); -/** - * Feature track that displays data generated from tool. - */ -var ToolDataFeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, {}); - - // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- - // is ready. - this.data_url = raw_data_url; - this.data_query_wait = 1000; - this.dataset_check_url = dataset_state_url; -}; - -extend(ToolDataFeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, { - /** - * For this track type, the predraw init sets up postdraw init. - */ - predraw_init: function() { - // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. - var track = this; - var post_init = function() { - if (track.data_manager.size() === 0) { - // Track still drawing initial data, so do nothing. - setTimeout(post_init, 300); - } - else { - // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start - // indexing. - track.data_url = default_data_url; - track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; - track.dataset_state_url = converted_datasets_state_url; - $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); - } - }; - post_init(); - } -}); - // Exports exports.View = View; @@ -3605,6 +3618,7 @@ exports.LineTrack = LineTrack; exports.FeatureTrack = FeatureTrack; exports.ReadTrack = ReadTrack; +exports.VcfTrack = VcfTrack; // End trackster_module encapsulation }; @@ -4173,20 +4187,20 @@ * Height of a single row, depends on mode */ get_row_height: function() { - var mode = this.mode, y_scale; + var mode = this.mode, height; if (mode === "Dense") { - y_scale = DENSE_TRACK_HEIGHT; + height = DENSE_TRACK_HEIGHT; } else if (mode === "no_detail") { - y_scale = NO_DETAIL_TRACK_HEIGHT; + height = NO_DETAIL_TRACK_HEIGHT; } else if (mode === "Squish") { - y_scale = SQUISH_TRACK_HEIGHT; + height = SQUISH_TRACK_HEIGHT; } else { // mode === "Pack" - y_scale = PACK_TRACK_HEIGHT; + height = PACK_TRACK_HEIGHT; } - return y_scale; + return height; }, /** @@ -4212,7 +4226,7 @@ ctx.globalAlpha = this.alpha_scaler.gen_val(feature); // In dense mode, put all data in top slot. - if (mode == "Dense") { + if (mode === "Dense") { slot = 1; } @@ -4375,104 +4389,44 @@ } }); - -var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) { - FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler); -} - -extend(VariantPainter.prototype, FeaturePainter.prototype, { - draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) { - var feature = data[i], - feature_uid = feature[0], - feature_start = feature[1], - feature_end = feature[2], - feature_name = feature[3], - // All features need a start, end, and vertical center. - f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), - f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), - y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, - thickness, y_start, thick_start = null, thick_end = null; - - if (no_label) { - ctx.fillStyle = block_color; - ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1); - } - else { // Show blocks, labels, etc. - // Unpack. - var ref_base = feature[4], alt_base = feature[5], qual = feature[6]; - - // Draw block for entry. - thickness = 9; - y_start = 1; - ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, thickness); - - // Add label for entry. - if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) { - // Draw label - ctx.fillStyle = label_color; - if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { - ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8); - } else { - ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8); - } - ctx.fillStyle = block_color; - } - - // Show additional data on block. - var vcf_label = ref_base + " / " + alt_base; - if (feature_start > tile_low && ctx.measureText(vcf_label).width < (f_end - f_start)) { - ctx.fillStyle = "white"; - ctx.textAlign = "center"; - ctx.fillText(vcf_label, left_offset + f_start + (f_end-f_start)/2, y_center + 8); - ctx.fillStyle = block_color; - } - } - - return [f_start, f_end]; - } -}); - var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) { FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler); this.ref_seq = (ref_seq ? ref_seq.data : null); }; -ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false }); - extend(ReadPainter.prototype, FeaturePainter.prototype, { /** - * Returns y_scale based on mode. + * Returns height based on mode. */ get_row_height: function() { - var y_scale, mode = this.mode; + var height, mode = this.mode; if (mode === "Dense") { - y_scale = DENSE_TRACK_HEIGHT; + height = DENSE_TRACK_HEIGHT; } else if (mode === "Squish") { - y_scale = SQUISH_TRACK_HEIGHT; + height = SQUISH_TRACK_HEIGHT; } else { // mode === "Pack" - y_scale = PACK_TRACK_HEIGHT; + height = PACK_TRACK_HEIGHT; if (this.prefs.show_insertions) { - y_scale *= 2; + height *= 2; } } - return y_scale; + return height; }, /** * Draw a single read. */ - draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { + draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) { ctx.textAlign = "center"; var track = this, tile_region = [tile_low, tile_high], base_offset = 0, seq_offset = 0, gap = 0, - char_width_px = ctx.canvas.manager.char_width_px; + char_width_px = ctx.canvas.manager.char_width_px, + block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color); // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -4519,7 +4473,7 @@ // Draw. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); if (gap > 0) { - ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = block_color; ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9); ctx.fillStyle = CONNECTOR_COLOR; // TODO: this can be made much more efficient by computing the complete sequence @@ -4537,7 +4491,7 @@ } } } else { - ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT); } @@ -4585,7 +4539,7 @@ draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]}; ctx.fillStyle = CONNECTOR_COLOR; // Based on overlap b/t sequence and tile, get sequence to be drawn. - switch(seq_tile_overlap) { + switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) { case(OVERLAP_START): seq = seq.slice(tile_low-seq_start); break; @@ -4616,7 +4570,7 @@ else { if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. - draw_last[draw_last.length] = {type: "text", data: [seq.length, insert_x_coord, y_center + 9]}; + draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); } else { // TODO: probably can merge this case with code above. @@ -4666,7 +4620,6 @@ f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, - block_color = this.prefs.block_color, label_color = this.prefs.label_color, // Left-gap for label text since we align chrom text to the position tick. gap = 0; @@ -4677,7 +4630,6 @@ } // Draw read. - ctx.fillStyle = block_color; if (feature[5] instanceof Array) { // Read is paired. var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ), @@ -4686,12 +4638,12 @@ b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ); // Draw left/forward read. - if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center); + if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) { + this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]); } // Draw right/reverse read. if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) { - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center); + this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]); } // Draw connector. if (b2_start > b1_end) { @@ -4700,10 +4652,9 @@ } } else { // Read is single. - ctx.fillStyle = block_color; - this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center); + this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); } - if (mode === "Pack" && feature_start > tile_low) { + if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") { // Draw label. ctx.fillStyle = this.prefs.label_color; // FIXME: eliminate tile_index @@ -4715,7 +4666,6 @@ ctx.textAlign = "right"; ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8); } - ctx.fillStyle = block_color; } // FIXME: provide actual coordinates for drawn read. @@ -4728,7 +4678,6 @@ exports.LinePainter = LinePainter; exports.LinkedFeaturePainter = LinkedFeaturePainter; exports.ReadPainter = ReadPainter; -exports.VariantPainter = VariantPainter; // End painters_module encapsulation }; diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -31,7 +31,7 @@ /** * Objects that can be added to a view. */ -var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup }; +var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "VcfTrack": VcfTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup }; /** * Decode a track from a dictionary. @@ -111,6 +111,9 @@ } } + // Need to update intro div after drawables have been added. + view.update_intro_div(); + // Set overview. var overview_track; for (var i = 0; i < view.drawables.length; i++) { @@ -154,14 +157,14 @@ break case 38: var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('-=' + change + 'px'); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); break; case 39: view.move_fraction(-0.25); break; case 40: var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('+=' + change + 'px'); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); break; } }); diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/admin/tool_shed_repository/browse_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -0,0 +1,127 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% from galaxy.web.base.controller import tool_shed_encode, tool_shed_decode %> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Installed tool shed repository '${repository.name}'</div> + <div class="toolFormBody"> + + %if tool_dicts: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Tools</b></td> + </tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td>${tool_dict[ 'name' ]}</div> + </td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if workflow_dicts: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Workflows</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>steps</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + <% index = 0 %> + %for wf_dict in workflow_dicts: + <% + full_path = wf_dict[ 'full_path' ] + workflow_dict = wf_dict[ 'workflow_dict' ] + workflow_name = workflow_dict[ 'name' ] + if 'steps' in workflow_dict: + ## Initially steps were not stored in the metadata record. + steps = workflow_dict[ 'steps' ] + else: + steps = [] + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %> + <tr> + <td> + <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> + ${workflow_name} + <div popupmenu="workflow-${index}-popup"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + </div> + </div> + </td> + <td> + %if 'steps' in workflow_dict: + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td> + </tr> + <% index += 1 %> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + </div> +</div> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/admin/tool_shed_repository/manage_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -0,0 +1,57 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin', action='browse_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <form name="edit_repository" id="edit_repository" action="${h.url_for( controller='admin', action='manage_tool_shed_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Tool shed:</label> + ${repository.tool_shed} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Name:</label> + ${repository.name} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="${description}" size="80"/> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Revision:</label> + ${repository.changeset_revision} + </div> + <div class="form-row"> + <label>Owner:</label> + ${repository.owner} + </div> + <div class="form-row"> + <label>Location:</label> + ${repo_files_dir} + </div> + <div class="form-row"> + <label>Deleted:</label> + ${repository.deleted} + </div> + <div class="form-row"> + <input type="submit" name="edit_repository_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,7 +42,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy" )} <script type="text/javascript"> // @@ -125,7 +125,7 @@ view = create_visualization( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), - JSON.parse('${ h.to_json_string( config['tracks'] ) }'), + JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'), JSON.parse('${ h.to_json_string( config['bookmarks'] ) }') ); init_editor(); diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako +++ b/templates/tracks/new_browser.mako @@ -19,7 +19,7 @@ </div><div class="form-row"> Is the build not listed here? - <a href="${h.url_for( controller='user', action='dbkeys', panels=True )}">Add a Custom Build</a> + <a href="${h.url_for( controller='user', action='dbkeys', use_panels=True )}">Add a Custom Build</a></div> %if default_dbkey is not None: <script type="text/javascript"> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -65,7 +65,7 @@ ${subscribe_check_box.get_html()} </div> %endif - %if user_type_fd_id_select_field: + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: <div class="form-row"><label>User type</label> ${user_type_fd_id_select_field.get_html()} diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -111,9 +111,13 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + </div> + <li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="tool_shed-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -34,9 +34,13 @@ <br/><br/><ul class="manage-table-actions"> %if webapp == 'galaxy': - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + </div> + <li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> + <div popupmenu="tool_shed-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a><a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -46,6 +46,9 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp=webapp )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp=webapp )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp=webapp )}" target="galaxy_main">Manage roles</a></div> + %if trans.app.config.allow_user_impersonation: + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate', webapp=webapp )}" target="galaxy_main">Impersonate a user</a></div> + %endif </div></div><div class="toolSectionPad"></div> @@ -64,7 +67,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> %if cloned_repositories: - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tool_shed_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </div></div> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -114,7 +114,7 @@ ['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] ] tab( "help", "Help", None, menu_options=menu_options) %> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/webapps/galaxy/user/info.mako --- a/templates/webapps/galaxy/user/info.mako +++ b/templates/webapps/galaxy/user/info.mako @@ -13,7 +13,7 @@ <div class="toolForm"><form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" ><div class="toolFormTitle">User information</div> - %if user_type_fd_id_select_field: + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: <div class="form-row"><label>User type:</label> ${user_type_fd_id_select_field.get_html()} diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -1,8 +1,8 @@ <%inherit file="/display_base.mako"/><%namespace file="/display_common.mako" import="render_message" /> -<% - from galaxy.tools.parameters import DataToolParameter, RuntimeValue +<%! + from galaxy.tools.parameters import DataToolParameter, RuntimeValue from galaxy.web import form_builder %> @@ -118,4 +118,4 @@ </tr> %endfor </table> -</%def> \ No newline at end of file +</%def> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 test-data/interpolate_result.bed --- /dev/null +++ b/test-data/interpolate_result.bed @@ -0,0 +1,219 @@ +chr1 27800000 29750669 6600000 0 1.7386 +chr1 29800669 34400000 6600000 0 1.7920 +chr1 46500000 51300000 4800000 0 1.4004 +chr1 102000000 103636494 5000000 0 1.2007 +chr1 103686494 103843838 5000000 0 NA +chr1 103893838 107000000 5000000 0 1.1883 +chr1 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25064047 25159219 2.18 +chr20 62108686 62284676 2.38 \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -175,6 +175,7 @@ <section name="Regional Variation" id="regVar"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> @@ -194,8 +195,10 @@ </section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /> + <tool file="regVariation/partialR_square.xml" /></section><section name="Multivariate Analysis" id="multVar"><tool file="multivariate_stats/pca.xml" /> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -70,6 +70,11 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/picard_index.loc" /></table> + <!-- Location of Picard dict files valid for GATK --> + <table name="gatk_picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path, tools_valid_for</columns> + <file path="tool-data/picard_index.loc" /> + </table><!-- Location of SRMA dict file and other files --><table name="srma_indexes" comment_char="#"><columns>value, dbkey, name, path</columns> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -11,6 +11,7 @@ -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/AnalyzeCovariates.jar" -recalFile "${input_recal}" -outputDir "${output_html.files_path}" + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R" diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -19,8 +19,8 @@ #end if --recal_file "${output_recal}" ${standard_covs} - #if $covariates.value: - #for $cov in $covariates.value: + #if str( $covariates ) != "None": + #for $cov in str( $covariates ).split( ',' ): -cov "${cov}" #end for #end if @@ -139,10 +139,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -13,6 +13,7 @@ -T "IndelRealigner" -o "${output_bam}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -50,13 +51,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -68,10 +72,16 @@ --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" @@ -108,10 +118,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -13,6 +13,7 @@ -T "RealignerTargetCreator" -o "${output_interval}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -104,10 +105,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -13,6 +13,7 @@ -T "TableRecalibration" -o "${output_bam}" -et "NO_ET" ##ET no phone home + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -118,10 +119,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -112,13 +112,13 @@ --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}" --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" ${analysis_param_type.doContextDependentGapPenalties} - #if $analysis_param_type.annotation.value: - #for $annotation in $analysis_param_type.annotation.value: + #if str( $analysis_param_type.annotation ) != "None": + #for $annotation in str( $analysis_param_type.annotation ).split( ','): --annotation "${annotation}" #end for #end if - #if $analysis_param_type.group.value: - #for $group in $analysis_param_type.group.value: + #if str( $analysis_param_type.group ) != "None": + #for $group in str( $analysis_param_type.group ).split( ','): --group "${group}" #end for #end if @@ -136,11 +136,11 @@ <param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options></param> @@ -396,7 +396,7 @@ <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /><data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /></outputs> - <!-- FIXME! <trackster_conf/> --> + <trackster_conf/><tests><test><param name="reference_source_selector" value="history" /> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -24,7 +24,7 @@ #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations": --useAllAnnotations #else: - #if $annotations_type.annotations.value: + #if str( $annotations_type.annotations ) != "None": #for $annotation in str( $annotations_type.annotations ).split( ',' ): --annotation "${annotation}" #end for @@ -127,7 +127,7 @@ ##end standard gatk options -p ' - #if $annotation_group.value: + #if str( $annotation_group ) != "None": #for $group in str( $annotation_group ).split( ',' ): --group "${group}" #end for @@ -146,10 +146,10 @@ <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" /><validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/> - <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --> + <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -102,7 +102,7 @@ <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -114,7 +114,7 @@ </param></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -159,7 +159,7 @@ <param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -106,7 +106,7 @@ <when value="cached"><param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -98,7 +98,7 @@ ##start analysis specific options -p ' - #if $annotations.value: + #if str( $annotations ) != "None": #for $annotation in str( $annotations ).split( ',' ): --use_annotation "${annotation}" #end for @@ -152,7 +152,7 @@ <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options></param> @@ -515,7 +515,7 @@ <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/><param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/><conditional name="bad_variant_selector"> - <param name="bad_variant_selector_type" type="select" label="Basic or Advanced Analysis options"> + <param name="bad_variant_selector_type" type="select" label="How to specify bad variants"><option value="percent" selected="True">Percent</option><option value="min_num">Number</option></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -12,6 +12,7 @@ -T "ValidateVariants" -et "NO_ET" ##ET no phone home + --num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" @@ -91,7 +92,7 @@ <when value="cached"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="ref_file" type="select" label="Using reference genome"> - <options from_data_table="picard_indexes"> + <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options></param> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -61,10 +61,10 @@ </param><when value="No"></when><when value="Use reference annotation"> - <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/></when><when value="Use reference annotation guide"> - <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/></when></conditional><conditional name="bias_correction"> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -4,7 +4,7 @@ picard_wrapper.py --input=$inputFile #if $source.indexSource == "built-in" - --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }" + --ref="${source.ref.fields.path}" #else --ref-file=$refFile --species-name=$source.speciesName diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/WeightedAverage.py --- /dev/null +++ b/tools/regVariation/WeightedAverage.py @@ -0,0 +1,103 @@ +#!/usr/bin/env python +""" + +usage: %prog bed_file_1 bed_file_2 out_file + -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file + -2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file +""" +from galaxy import eggs + +import collections +import sys, string +#import numpy +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +import sys, traceback, fileinput +from warnings import warn +from galaxy.tools.util.galaxyops import * +from bx.cookbook import doc_optparse + + +#export PYTHONPATH=~/galaxy/lib/ +#running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + + +def FindRate(chromosome,start_stop,dictType): + OverlapList=[] + for tempO in dictType[chromosome]: + DatabaseInterval=[tempO[0],tempO[1]] + Overlap=GetOverlap(start_stop,DatabaseInterval) + if Overlap>0: + OverlapList.append([Overlap,tempO[2]]) + + if len(OverlapList)>0: + + SumRecomb=0 + SumOverlap=0 + for member in OverlapList: + SumRecomb+=member[0]*member[1] + SumOverlap+=member[0] + averageRate=SumRecomb/SumOverlap + + return averageRate + + else: + return 'NA' + + + +def GetOverlap(a,b): + return min(a[1],b[1])-max(a[0],b[0]) + +options, args = doc_optparse.parse( __doc__ ) + +try: + chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 ) + chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 ) + input1, input2, input3 = args +except Exception, eee: + print eee + stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." ) + + + +fd2=open(input2) +lines2=fd2.readlines() +RecombChrDict=collections.defaultdict(list) + +skipped=0 +for line in lines2: + temp=line.strip().split() + try: + assert float(temp[int(name_col_2)]) + except: + skipped+=1 + continue + tempIndex=[int(temp[int(start_col_2)]),int(temp[int(end_col_2)]),float(temp[int(name_col_2)])] + RecombChrDict[temp[int(chr_col_2)]].append(tempIndex) + +print "Skipped %d features with invalid values" %(skipped) + +fd1=open(input1) +lines=fd1.readlines() +finalProduct='' +for line in lines: + temp=line.strip().split('\t') + chromosome=temp[int(chr_col_1)] + start=int(temp[int(start_col_1)]) + stop=int(temp[int(end_col_1)]) + start_stop=[start,stop] + RecombRate=FindRate(chromosome,start_stop,RecombChrDict) + try: + RecombRate="%.4f" %(float(RecombRate)) + except: + RecombRate=RecombRate + finalProduct+=line.strip()+'\t'+str(RecombRate)+'\n' +fdd=open(input3,'w') +fdd.writelines(finalProduct) +fdd.close() diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/WeightedAverage.xml --- /dev/null +++ b/tools/regVariation/WeightedAverage.xml @@ -0,0 +1,71 @@ +<tool id="wtavg" name="Assign weighted-average" version="1.0.0"> + <description> of the values of features overlapping an interval </description> + <command interpreter="python">WeightedAverage.py $genomic_interval $genomic_feature $out_file1 -1 ${genomic_interval.metadata.chromCol},${genomic_interval.metadata.startCol},${genomic_interval.metadata.endCol},${genomic_interval.metadata.strandCol} -2 ${genomic_feature.metadata.chromCol},${genomic_feature.metadata.startCol},${genomic_feature.metadata.endCol},${genomic_feature.metadata.strandCol},${genomic_feature.metadata.nameCol}</command> + + <inputs> + <param format="interval" name="genomic_interval" type="data" label="Genomic intervals (first dataset)" help="Dataset missing? See Note below."/> + <param format="interval" name="genomic_feature" label="Genomic features (second dataset)" type="data" help="Make sure the value column is specified. See Note below." /> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="genomic_interval" /> + </outputs> + <tests> + <!-- Test data with valid values --> + <test> + <param name="genomic_interval" value="interval_interpolate.bed"/> + <param name="genomic_feature" value="value_interpolate.bed"/> + <output name="out_file1" file="interpolate_result.bed"/> + </test> + + </tests> + <help> + + +.. class:: infomark + +**What it does** + +For each interval in your first dataset, this tool calculates the weighted average value of the overlapping features in your second dataset. + +- When a genomic interval partially or totally overlaps a single genomic feature, the value of that genomic feature is assigned to the genomic interval. +- When a genomic interval partially or totally overlaps with more than one genomic features, the average of the values of the overlapping genomic features weighted by the corresponding number of overlapping bases is assigned to the genomic interval. +- When a genomic interval does not overlap with any genomic feature, 'NA' will be assigned as it's value. + +----- + +.. class:: warningmark + +**Note** + +The input datasets should be in **bed** or **interval** format. Please use "edit attributes"/pencil icon to specify the column containing the values for the features in the second dataset as **name/identifier** column. + +The output will contain all the columns in the first input plus a new column containing the assigned value for each interval. + +----- + +**Example** + +- Suppose our first dataset contains the following **genomic intervals**:: + + chr start stop + chr1 1000 2000 + chr1 3000 5000 + chr1 8000 9000 + +- and our second dataset contains the following **genomic features** each having an associated value (in fourth column) :: + + chr start stop name + chr1 900 1200 0.5 + chr1 2900 3100 0.2 + chr1 4800 5100 0.8 + +- For each **genomic interval** in our first dataset, this tool calculates the weighted average value of the overlapping **genomic features** in our second dataset :: + + chr1 1000 2000 0.5 + chr1 3000 5000 0.6 + chr1 8000 9000 NA + + + +</help> +</tool> \ No newline at end of file diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/logistic_regression_vif.py --- /dev/null +++ b/tools/regVariation/logistic_regression_vif.py @@ -0,0 +1,185 @@ +#!/usr/bin/env python + +from galaxy import eggs +import sys, string +from rpy import * +import numpy + +#export PYTHONPATH=~/galaxy/lib/ + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() +#infile = 'logreg_inp.tab' +#y_col=3 +#x_cols=[1,2,3] +#outfile='logreg_out.txt' +#python logistic_regression_vif.py logreg_inp.tab 4 1,2,3 logreg_out2.tabular # running test +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] + + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') +elems = [] +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except: + yval = r('NA') + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except: + xval = r('NA') + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() + +check1=0 +check0=0 +for i in y_vals: + if i == 1: + check1=1 + if i == 0: + check0=1 +if check1==0 or check0==0: + sys.exit("Warning: logistic regression must have at least two classes") + +for i in y_vals: + if i not in [1,0,r('NA')]: + print >>fout, str(i) + sys.exit("Warning: the current version of this tool can run only with two classes and need to be labeled as 0 and 1.") + + +dat= r.list(x=array(x_vals1), y=y_vals) +novif=0 +set_default_mode(NO_CONVERSION) +try: + linear_model = r.glm(r("y ~ x"), data = r.na_exclude(dat),family="binomial") + #r('library(car)') + #r.assign('dat',dat) + #r.assign('ncols',len(x_cols)) + #r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')).as_py() + +except RException, rex: + stop_err("Error performing logistic regression on the input data.\nEither the response column or one of the predictor columns contain only non-numeric or invalid values.") +if len(x_cols)>1: + try: + + r('library(car)') + r.assign('dat',dat) + r.assign('ncols',len(x_cols)) + vif=r.vif(r('glm(dat$y ~ ., data = na.exclude(data.frame(as.matrix(dat$x,ncol=ncols))->datx),family="binomial")')) + except RException, rex: + print rex +else: + novif=1 + +set_default_mode(BASIC_CONVERSION) + +coeffs=linear_model.as_py()['coefficients'] +null_deviance=linear_model.as_py()['null.deviance'] +residual_deviance=linear_model.as_py()['deviance'] +yintercept= coeffs['(Intercept)'] +summary = r.summary(linear_model) +co = summary.get('coefficients', 'NA') +""" +if len(co) != len(x_vals)+1: + stop_err("Stopped performing logistic regression on the input data, since one of the predictor columns contains only non-numeric or invalid values.") +""" + +try: + yintercept = r.round(float(yintercept), digits=10) + pvaly = r.round(float(co[0][3]), digits=10) +except: + pass +print >>fout, "response column\tc%d" %(y_col+1) +tempP=[] +for i in x_cols: + tempP.append('c'+str(i+1)) +tempP=','.join(tempP) +print >>fout, "predictor column(s)\t%s" %(tempP) +print >>fout, "Y-intercept\t%s" %(yintercept) +print >>fout, "p-value (Y-intercept)\t%s" %(pvaly) + +if len(x_vals) == 1: #Simple linear regression case with 1 predictor variable + try: + slope = r.round(float(coeffs['x']), digits=10) + except: + slope = 'NA' + try: + pval = r.round(float(co[1][3]), digits=10) + except: + pval = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[0]+1,slope) + print >>fout, "p-value (c%d)\t%s" %(x_cols[0]+1,pval) +else: #Multiple regression case with >1 predictors + ind=1 + while ind < len(coeffs.keys()): + try: + slope = r.round(float(coeffs['x'+str(ind)]), digits=10) + except: + slope = 'NA' + print >>fout, "Slope (c%d)\t%s" %(x_cols[ind-1]+1,slope) + try: + pval = r.round(float(co[ind][3]), digits=10) + except: + pval = 'NA' + print >>fout, "p-value (c%d)\t%s" %(x_cols[ind-1]+1,pval) + ind+=1 + +rsq = summary.get('r.squared','NA') + + +try: + rsq= r.round(float((null_deviance-residual_deviance)/null_deviance), digits=5) + null_deviance= r.round(float(null_deviance), digits=5) + residual_deviance= r.round(float(residual_deviance), digits=5) + + #rsq = r.round(float(rsq), digits=5) + +except: + pass + +print >>fout, "Null deviance\t%s" %(null_deviance) +print >>fout, "Residual deviance\t%s" %(residual_deviance) +print >>fout, "pseudo R-squared\t%s" %(rsq) +print >>fout, "\n" +print >>fout, 'vif' + +if novif==0: + py_vif=vif.as_py() + count=0 + for i in sorted(py_vif.keys()): + print >>fout,'c'+str(x_cols[count]+1) ,str(py_vif[i]) + count+=1 +elif novif==1: + print >>fout, "vif can calculate only when model have more than 1 predictor" diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/logistic_regression_vif.xml --- /dev/null +++ b/tools/regVariation/logistic_regression_vif.xml @@ -0,0 +1,74 @@ +<tool id="LogisticRegression" name="Perform Logistic Regression with vif" version="1.0.1"> + <description></description> + <command interpreter="python"> + logistic_regression_vif.py + $input1 + $response_col + $predictor_cols + $out_file1 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" numerical="True"/> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" numerical="True" multiple="true" > + <validator type="no_options" message="Please select at least one column."/> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> + <test> + <param name="input1" value="logreg_inp.tabular"/> + <param name="response_col" value="4"/> + <param name="predictor_cols" value="1,2,3"/> + <output name="out_file1" file="logreg_out2.tabular"/> + + </test> + </tests> + <help> + + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool uses the **'glm'** function from R statistical package to perform logistic regression on the input data. It outputs one file containing the summary statistics of the performed regression. Also, it calculates VIF(Variance Inflation Factor) with **'vif'** function from library (car) in R. + + +*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.* + +----- + +.. class:: warningmark + +**Note** + +- This tool currently treats all predictor variables as continuous numeric variables and response variable as categorical variable. Currently, the response variable can have only two classes, namely 0 and 1. The program will take 0 as base class. + +- Rows containing non-numeric (or missing) data in any of the chosen columns will be skipped from the analysis. + +- The summary statistics in the output are described below: + +- Pseudo R-squared: the proportion of model improvement from null model +- p-value: p-value for the z-test of the null hypothesis that the corresponding slope is equal to zero against the two-sided alternative. +- Coefficient indicates log ratio of (probability to be class 1 / probability to be class 0) + +- This tool also provides **Variance Inflation Factor or VIF** which quantifies the level of multicollinearity. The tool will automatic generate VIF if the model has more than one predictor. The higher the VIF, the higher is the multicollinearity. Multicollinearity will inflate standard error and reduce level of significance of the predictor. In the worst case, it can reverse direction of slope for highly correlated predictors if one of them is significant. A general thumb-rule is to use those predictors having VIF lower than 10 or 5. +- **vif** is calculated by + - First, regressing each predictor over all other predictors, and recording R-squared for each regression. + - Second, computing vif as 1/(1- R_squared) + + </help> +</tool> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/partialR_square.py --- /dev/null +++ b/tools/regVariation/partialR_square.py @@ -0,0 +1,146 @@ +#!/usr/bin/env python + +from galaxy import eggs + +import sys, string +from rpy import * +import numpy + +#export PYTHONPATH=~/galaxy/lib/ +#running command python partialR_square.py reg_inp.tab 4 1,2,3 partialR_result.tabular + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def sscombs(s): + if len(s) == 1: + return [s] + else: + ssc = sscombs(s[1:]) + return [s[0]] + [s[0]+comb for comb in ssc] + ssc + + +infile = sys.argv[1] +y_col = int(sys.argv[2])-1 +x_cols = sys.argv[3].split(',') +outfile = sys.argv[4] + +print "Predictor columns: %s; Response column: %d" %(x_cols,y_col+1) +fout = open(outfile,'w') + +for i, line in enumerate( file ( infile )): + line = line.rstrip('\r\n') + if len( line )>0 and not line.startswith( '#' ): + elems = line.split( '\t' ) + break + if i == 30: + break # Hopefully we'll never get here... + +if len( elems )<1: + stop_err( "The data in your input dataset is either missing or not formatted properly." ) + +y_vals = [] +x_vals = [] + +for k,col in enumerate(x_cols): + x_cols[k] = int(col)-1 + x_vals.append([]) + """ + try: + float( elems[x_cols[k]] ) + except: + try: + msg = "This operation cannot be performed on non-numeric column %d containing value '%s'." %( col, elems[x_cols[k]] ) + except: + msg = "This operation cannot be performed on non-numeric data." + stop_err( msg ) + """ +NA = 'NA' +for ind,line in enumerate( file( infile )): + if line and not line.startswith( '#' ): + try: + fields = line.split("\t") + try: + yval = float(fields[y_col]) + except Exception, ey: + yval = r('NA') + #print >>sys.stderr, "ey = %s" %ey + y_vals.append(yval) + for k,col in enumerate(x_cols): + try: + xval = float(fields[col]) + except Exception, ex: + xval = r('NA') + #print >>sys.stderr, "ex = %s" %ex + x_vals[k].append(xval) + except: + pass + +x_vals1 = numpy.asarray(x_vals).transpose() +dat= r.list(x=array(x_vals1), y=y_vals) + +set_default_mode(NO_CONVERSION) +try: + full = r.lm(r("y ~ x"), data= r.na_exclude(dat)) #full model includes all the predictor variables specified by the user +except RException, rex: + stop_err("Error performing linear regression on the input data.\nEither the response column or one of the predictor columns contain no numeric values.") +set_default_mode(BASIC_CONVERSION) + +summary = r.summary(full) +fullr2 = summary.get('r.squared','NA') + +if fullr2 == 'NA': + stop_error("Error in linear regression") + +if len(x_vals) < 10: + s = "" + for ch in range(len(x_vals)): + s += str(ch) +else: + stop_err("This tool only works with less than 10 predictors.") + +print >>fout, "#Model\tR-sq\tpartial_R_Terms\tpartial_R_Value" +all_combos = sorted(sscombs(s), key=len) +all_combos.reverse() +for j,cols in enumerate(all_combos): + #if len(cols) == len(s): #Same as the full model above + # continue + if len(cols) == 1: + x_vals1 = x_vals[int(cols)] + else: + x_v = [] + for col in cols: + x_v.append(x_vals[int(col)]) + x_vals1 = numpy.asarray(x_v).transpose() + dat= r.list(x=array(x_vals1), y=y_vals) + set_default_mode(NO_CONVERSION) + red = r.lm(r("y ~ x"), data= dat) #Reduced model + set_default_mode(BASIC_CONVERSION) + summary = r.summary(red) + redr2 = summary.get('r.squared','NA') + try: + partial_R = (float(fullr2)-float(redr2))/(1-float(redr2)) + except: + partial_R = 'NA' + col_str = "" + for col in cols: + col_str = col_str + str(int(x_cols[int(col)]) + 1) + " " + col_str.strip() + partial_R_col_str = "" + for col in s: + if col not in cols: + partial_R_col_str = partial_R_col_str + str(int(x_cols[int(col)]) + 1) + " " + partial_R_col_str.strip() + if len(cols) == len(s): #full model + partial_R_col_str = "-" + partial_R = "-" + try: + redr2 = "%.4f" %(float(redr2)) + except: + pass + try: + partial_R = "%.4f" %(float(partial_R)) + except: + pass + print >>fout, "%s\t%s\t%s\t%s" %(col_str,redr2,partial_R_col_str,partial_R) diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/regVariation/partialR_square.xml --- /dev/null +++ b/tools/regVariation/partialR_square.xml @@ -0,0 +1,68 @@ +<tool id="partialRsq" name="Compute partial R square" version="1.0.0"> + <description></description> + <command interpreter="python"> + partialR_square.py + $input1 + $response_col + $predictor_cols + $out_file1 + 1>/dev/null + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" /> + <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true"> + <validator type="no_options" message="Please select at least one column."/> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input1" /> + </outputs> + <requirements> + <requirement type="python-module">rpy</requirement> + </requirements> + <tests> + <!-- Test data with vlid values --> + <test> + <param name="input1" value="regr_inp.tabular"/> + <param name="response_col" value="3"/> + <param name="predictor_cols" value="1,2"/> + <output name="out_file1" file="partialR_result.tabular"/> + </test> + + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Edit Datasets->Convert characters* + +----- + +.. class:: infomark + +**What it does** + +This tool computes the Partial R squared for all possible variable subsets using the following formula: + +**Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, which denotes the case where the 'i'th predictor is dropped. + + + +In general, **Partial R squared = [SSE(without i: 1,2,...,p-1) - SSE (full: 1,2,..,i..,p-1) / SSE(without i: 1,2,...,p-1)]**, where, + +- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the full set of predictors SSE(X1, X2 … Xp) +- SSE (full: 1,2,..,i..,p-1) = Sum of Squares left out by the set of predictors excluding; for example, if we omit the first predictor, it will be SSE(X2 … Xp). + + +The 4 columns in the output are described below: + +- Column 1 (Model): denotes the variables present in the model +- Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1 +- Column 3 (Partial R squared_Terms): denotes the variable/s for which Partial R squared is computed. These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model. +- Column 4 (Partial R squared): denotes the Partial R squared value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model. + +*R Development Core Team (2010). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.* + + </help> +</tool> diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/sr_mapping/srma_wrapper.py --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -29,7 +29,7 @@ parser = optparse.OptionParser() parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to index and use' ) parser.add_option( '-u', '--refUID', dest='refUID', help='The pre-index reference genome unique Identifier' ) - parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' ) + #parser.add_option( '-L', '--refLocations', dest='refLocations', help='The filepath to the srma indices location file' ) parser.add_option( '-i', '--input', dest='input', help='The SAM/BAM input file' ) parser.add_option( '-I', '--inputIndex', dest='inputIndex', help='The SAM/BAM input index file' ) parser.add_option( '-o', '--output', dest='output', help='The SAM/BAM output file' ) diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 tools/sr_mapping/srma_wrapper.xml --- a/tools/sr_mapping/srma_wrapper.xml +++ b/tools/sr_mapping/srma_wrapper.xml @@ -4,9 +4,9 @@ #if $refGenomeSource.refGenomeSource_type == "history": --ref=$refGenomeSource.ownFile #else: - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.ref.fields.path}" --refUID=$refGenomeSource.ref - --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc + ##--refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc #end if --input=$input --inputIndex=${input.metadata.bam_index} diff -r 42c8a6cfaa5b76204e978eedfd17647b05531b13 -r f05722e66a8a42e75f01a29b723ed50525e77e55 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -405,6 +405,9 @@ # Allow administrators to delete accounts. #allow_user_deletion = False +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + # Allow users to remove their datasets from disk immediately (otherwise, # datasets will be removed after a time period specified by an administrator in # the cleanup scripts run via cron) https://bitbucket.org/galaxy/galaxy-central/changeset/b1a8b03710fe/ changeset: b1a8b03710fe user: natefoo date: 2011-11-08 18:20:06 summary: Actual user: Fix for ownership problems when using splitting. affected #: 3 files diff -r f05722e66a8a42e75f01a29b723ed50525e77e55 -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -530,19 +530,11 @@ self.sa_session.expunge_all() job = self.get_job() - if self.app.config.drmaa_external_runjob_script and job.user is not None: - try: - # FIXME: hardcoded path - cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ] - log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) - p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) - p.wait() - assert p.returncode == 0 - except: - # TODO: log stdout/stderr - log.exception( '(%s) Failed to change ownership of %s, failing' % ( job.id, self.working_directory ) ) - self.fail( job.info ) - return + try: + self.reclaim_ownership() + except: + self.fail( job.info ) + log.exception( '(%s) Failed to change ownership of %s, failing' % ( job.id, self.working_directory ) ) # if the job was deleted, don't finish it if job.state == job.states.DELETED: @@ -900,25 +892,38 @@ else: return 'anonymous@unknown' + def _change_ownership( self, username, gid ): + job = self.get_job() + # FIXME: hardcoded path + cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, username, str( gid ) ] + log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) + p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + # TODO: log stdout/stderr + stdout, stderr = p.communicate() + assert p.returncode == 0 + def change_ownership_for_run( self ): job = self.get_job() if self.app.config.external_chown_script and job.user is not None: try: - # FIXME: hardcoded path - cmd = [ '/usr/bin/sudo', '-E', self.app.config.external_chown_script, self.working_directory, self.user_system_pwent[0], str( self.user_system_pwent[3] ) ] - log.debug( '(%s) Changing ownership of working directory with: %s' % ( job.id, ' '.join( cmd ) ) ) - p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) - stdout, stderr = p.communicate() - assert p.returncode == 0 + self._change_ownership( self.user_system_pwent[0], str( self.user_system_pwent[3] ) ) except: log.exception( '(%s) Failed to change ownership of %s, making world-writable instead' % ( job.id, self.working_directory ) ) os.chmod( self.working_directory, 0777 ) + def reclaim_ownership( self ): + job = self.get_job() + if self.app.config.external_chown_script and job.user is not None: + self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) + @property def user_system_pwent( self ): if self.__user_system_pwent is None: job = self.get_job() - self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] ) + try: + self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] ) + except: + pass return self.__user_system_pwent @property diff -r f05722e66a8a42e75f01a29b723ed50525e77e55 -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -109,6 +109,10 @@ if sleep_time < 8: sleep_time *= 2 + import time + + job_wrapper.reclaim_ownership() # if running as the actual user, change ownership before merging. + log.debug('execution finished - beginning merge: %s' % command_line) stdout, stderr = splitter.do_merge(job_wrapper, task_wrappers) diff -r f05722e66a8a42e75f01a29b723ed50525e77e55 -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 lib/galaxy/jobs/splitters/multi.py --- a/lib/galaxy/jobs/splitters/multi.py +++ b/lib/galaxy/jobs/splitters/multi.py @@ -46,7 +46,7 @@ pass # pass original file name else: log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name) - log.error(log_error) + log.exception(log_error) raise Exception(log_error) if len(type_to_input_map) > 1: @@ -138,7 +138,7 @@ pickone_done.append(output) else: log_error = "The output '%s' does not define a method for implementing parallelism" % output - log.error(log_error) + log.exception(log_error) raise Exception(log_error) except Exception, e: stdout = 'Error merging files'; https://bitbucket.org/galaxy/galaxy-central/changeset/d24b1a15ab0a/ changeset: d24b1a15ab0a user: natefoo date: 2011-11-16 19:40:46 summary: Merge. affected #: 225 files diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -9,7 +9,7 @@ <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/><display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /> - <!-- <display file="igv/bam.xml" /> --> + <display file="igv/bam.xml" /></datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> @@ -88,7 +88,7 @@ <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/><datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/><datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/> - <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/><datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"><converter file="interval_to_bed_converter.xml" target_datatype="bed"/> @@ -154,8 +154,10 @@ <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <display file="igv/vcf.xml" /></datatype><datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> @@ -164,10 +166,14 @@ <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/><!-- <display file="gbrowse/gbrowse_wig.xml" /> --></datatype> - <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /> - <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> - <datatype extension="tabix" type="galaxy.datatypes.data:Data" /> - <datatype extension="bgzip" type="galaxy.datatypes.data:Data" /> + <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype><!-- Start EMBOSS tools --><datatype extension="acedb" type="galaxy.datatypes.data:Text"/><datatype extension="asn1" type="galaxy.datatypes.data:Text"/> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -1,12 +1,32 @@ +<?xml version="1.0"?><display id="igv_bam" version="1.0.0" name="display with IGV"> - <link id="web" name="web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> + + <!-- Load links from file: one line to one link --> + <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + + <!-- Define parameters by column from file, allow splitting on builds --> + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + + <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> + <filter>${dataset.dbkey in $site_dbkeys}</filter> + + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> + <url>${redirect_url}</url> + + <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> + <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + </param> + + <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> <jnlp spec="1.0+" - codebase="http://www.broadinstitute.org/igvdata/jws/prod">; + codebase="${site_link}"> <information> <title>IGV 1.5</title> <vendor>The Broad Institute</vendor> @@ -54,17 +74,22 @@ <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> <argument>-g</argument> - <argument>${bam_file.dbkey}</argument> + <argument>${site_organism}</argument> <argument>${bam_file.url}</argument> </application-desc> </jnlp> - </param> - </link> - - <link id="local" name="local"> - <url>http://localhost:60151/load?file=${qp($bam_file.url)}&genome=${qp($bam_file.dbkey)}&merge=true</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - </link> + <param type="template" name="redirect_url" strip="True" > + #if $site_id.startswith( 'local_' ) + ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true + #elif $site_id.startswith( 'web_link_' ): + ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true + #else: + ${jnlp.url} + #end if + </param> + </dynamic_links> + + </display> +<!-- Dan Blankenberg --> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca display_applications/igv/vcf.xml --- /dev/null +++ b/display_applications/igv/vcf.xml @@ -0,0 +1,95 @@ +<?xml version="1.0"?> +<display id="igv_vcf" version="1.0.0" name="display with IGV"> + + <!-- Load links from file: one line to one link --> + <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + + <!-- Define parameters by column from file, allow splitting on builds --> + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + + <!-- Filter out some of the links based upon matching site_dbkeys to dataset dbkey --> + <filter>${dataset.dbkey in $site_dbkeys}</filter> + + <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name --> + <url>${redirect_url}</url> + + <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" /> + <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + </param> + + <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> +<jnlp + spec="1.0+" + codebase="${site_link}"> + <information> + <title>IGV 1.5</title> + <vendor>The Broad Institute</vendor> + <homepage href="http://www.broadinstitute.org/igv"/>; + <description>IGV Software</description> + <description kind="short">IGV</description> + </information> + <security> + <all-permissions/> + </security> + <resources> + +<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> + <jar href="igv.jar" download="eager" main="true"/> + <jar href="batik-codec.jar" download="eager"/> + <property name="apple.laf.useScreenMenuBar" value="true"/> + <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> + <property name="com.apple.mrj.application.live-resize" value="true"/> + <property name="com.apple.macos.smallTabs" value="true"/> + </resources> + + <resources os="Mac" arch="i386"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macintel.jar"/> + </resources> + + <resources os="Mac" arch="ppc"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Mac" arch="PowerPC"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Windows"> + <property name="sun.java2d.noddraw" value="true"/> + <nativelib href="hdfnative-win.jar"/> + </resources> + + <resources os="Linux"> + <nativelib href="hdfnative-linux64.jar"/> + </resources> + + <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> + <argument>-g</argument> + <argument>${site_organism}</argument> + <argument>${bgzip_file.url}</argument> + </application-desc> +</jnlp> + </param> + <param type="template" name="redirect_url" strip="True" > + #if $site_id.startswith( 'local_' ) + ${site_link}?file=${bgzip_file.qp}&genome=${site_organism}&merge=true + #elif $site_id.startswith( 'web_link_' ): + ${site_link}?sessionURL=${bgzip_file.qp}&genome=${site_organism}&merge=true + #else: + ${jnlp.url} + #end if + </param> + </dynamic_links> + + +</display> +<!-- Dan Blankenberg --> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -12,7 +12,7 @@ no_auto = pbs_python DRMAA_python [eggs:platform] -bx_python = 0.7.0 +bx_python = 0.7.1 Cheetah = 2.2.2 ctypes = 1.0.2 DRMAA_python = 0.2 @@ -67,7 +67,7 @@ psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _494c2d1d68b3_rebuild1 +bx_python = _7b95ff194725 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_b10f6e722e9a diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -26,7 +26,7 @@ """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'binary data' - dataset.blurb = 'data' + dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_summary_tree_converter.py @@ -50,4 +50,4 @@ st.write(out_fname) if __name__ == "__main__": - main() \ No newline at end of file + main() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_bgzip_to_tabix_0" name="Convert BGZ VCF to tabix" version="1.0.0" hidden="true"> +<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <command interpreter="python">interval_to_tabix_converter.py 'vcf' '' '$input1' '$output1'</command> + <inputs> + <page> + <param format="vcf_bgzip" name="input1" type="data" label="Choose BGZIP'd VCF file"/> + </page> + </inputs> + <outputs> + <data format="tabix" name="output1"/> + </outputs> + <help> + </help> +</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.0" hidden="true"> +<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <command interpreter="python">bgzip.py vcf $input1 $output1</command> + <inputs> + <page> + <param format="vcf" name="input1" type="data" label="Choose Vcf file"/> + </page> + </inputs> + <outputs> + <data format="vcf_bgzip" name="output1"/> + </outputs> + <help> + </help> +</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -46,18 +46,22 @@ try: extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) + type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) display_in_upload = elem.get( 'display_in_upload', False ) make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - if extension and dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) + if extension and ( dtype or type_extension ): + if dtype: + fields = dtype.split( ':' ) + datatype_module = fields[0] + datatype_class_name = fields[1] + fields = datatype_module.split( '.' ) + module = __import__( fields.pop(0) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) + elif type_extension: + datatype_class = self.datatypes_by_extension[type_extension].__class__ if make_subclass: datatype_class = type( datatype_class_name, (datatype_class,), {} ) self.datatypes_by_extension[extension] = datatype_class() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -554,7 +554,7 @@ self.version_string = open(version_filename).read() os.unlink(version_filename) - if self.app.config.outputs_to_working_directory: + if self.app.config.outputs_to_working_directory and not self.__link_file_check(): for dataset_path in self.get_output_fnames(): try: shutil.move( dataset_path.false_path, dataset_path.real_path ) @@ -604,7 +604,7 @@ dataset.blurb = 'done' dataset.peek = 'no peek' - dataset.info = context['stdout'] + context['stderr'] + dataset.info = ( dataset.info or '' ) + context['stdout'] + context['stderr'] dataset.tool_version = self.version_string dataset.set_size() if context['stderr']: @@ -892,6 +892,15 @@ else: return 'anonymous@unknown' + def __link_file_check( self ): + """ outputs_to_working_directory breaks library uploads where data is + linked. This method is a hack that solves that problem, but is + specific to the upload tool and relies on an injected job param. This + method should be removed ASAP and replaced with some properly generic + and stateful way of determining link-only datasets. -nate + """ + return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files' + def _change_ownership( self, username, gid ): job = self.get_job() # FIXME: hardcoded path diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py +++ b/lib/galaxy/tools/actions/upload.py @@ -25,4 +25,4 @@ json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] - return upload_common.create_job( trans, incoming, tool, json_file_path, data_list, return_job=True ) + return upload_common.create_job( trans, incoming, tool, json_file_path, data_list ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -300,7 +300,7 @@ if trans.app.config.drmaa_external_runjob_script: os.chmod(json_file_path, 0777) return json_file_path -def create_job( trans, params, tool, json_file_path, data_list, folder=None, return_job=False ): +def create_job( trans, params, tool, json_file_path, data_list, folder=None ): """ Create the upload job. """ @@ -352,10 +352,7 @@ output = odict() for i, v in enumerate( data_list ): output[ 'output%i' % i ] = v - if return_job: - return job, output - else: - return output + return job, output def active_folders( trans, folder ): # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). # Much faster way of retrieving all active sub-folders within a given folder than the diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -164,9 +164,14 @@ @classmethod def build( cls, tool, param ): """Factory method to create parameter of correct type""" + param_name = param.get( "name" ) + if not param_name: + raise ValueError( "Tool parameters require a 'name'" ) param_type = param.get("type") - if not param_type or param_type not in parameter_types: - raise ValueError( "Unknown tool parameter type '%s'" % param_type ) + if not param_type: + raise ValueError( "Tool parameter '%s' requires a 'type'" % ( param_name ) ) + elif param_type not in parameter_types: + raise ValueError( "Tool parameter '%s' uses an unknown type '%s'" % ( param_name, param_type ) ) else: return parameter_types[param_type]( tool, param ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -574,11 +574,9 @@ """ Sends an email. """ - header_to = to - if isinstance( to, list ): - header_to = ', '.join( to ) + to = listify( to ) msg = MIMEText( body ) - msg[ 'To' ] = header_to + msg[ 'To' ] = ', '.join( to ) msg[ 'From' ] = frm msg[ 'Subject' ] = subject if config.smtp_server is None: @@ -609,12 +607,10 @@ log.error( "The server didn't accept the username/password combination: %s" % e ) s.close() raise - except smtplib.SMTPError, e: + except smtplib.SMTPException, e: log.error( "No suitable authentication method was found: %s" % e ) s.close() raise - if isinstance( to, basestring ): - to = [ to ] s.sendmail( frm, to, msg.as_string() ) s.quit() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -2,14 +2,15 @@ Data providers for tracks visualizations. """ -import sys -from math import ceil, log +import sys, time +from math import ceil, log, sqrt import pkg_resources pkg_resources.require( "bx-python" ) if sys.version_info[:2] == (2, 4): pkg_resources.require( "ctypes" ) pkg_resources.require( "pysam" ) pkg_resources.require( "numpy" ) +import numpy from galaxy.datatypes.util.gff_util import * from galaxy.util.json import from_json_string from bx.interval_index_file import Indexes @@ -362,14 +363,18 @@ for large datasets. """ - def get_iterator( self, chrom, start, end ): + def get_iterator( self, chrom=None, start=None, end=None ): def line_filter_iter(): for line in open( self.original_dataset.file_name ): + if line.startswith( "track" ) or line.startswith( "browser" ): + continue feature = line.split() feature_chrom = feature[0] feature_start = int( feature[1] ) feature_end = int( feature[2] ) - if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ): + if ( chrom is not None and feature_chrom != chrom ) \ + or ( start is not None and feature_start > int( end ) ) \ + or ( end is not None and feature_end < int( start ) ): continue yield line return line_filter_iter() @@ -740,40 +745,73 @@ # Bigwig has the possibility of it being a standalone bigwig file, in which case we use # original_dataset, or coming from wig->bigwig conversion in which we use converted_dataset f, bbi = self._get_dataset() - + + # If the stats kwarg was provide, we compute overall summary data for + # the entire chromosome, but no reduced data -- currently only + # providing values used by trackster to determine the default range if 'stats' in kwargs: - all_dat = bbi.query(chrom, 0, 2147483647, 1) + # FIXME: use actual chromosome size + summary = bbi.summarize( chrom, 0, 214783647, 1 ) f.close() - if all_dat is None: + if summary is None: return None - - all_dat = all_dat[0] # only 1 summary - return { 'data' : { 'max': float( all_dat['max'] ), \ - 'min': float( all_dat['min'] ), \ - 'total_frequency': float( all_dat['coverage'] ) } \ - } - + else: + # Does the summary contain any defined values? + valid_count = summary.valid_count[0] + if summary.valid_count < 1: + return None + + # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower + # bounds that contain ~95% of the data. + mean = summary.sum_data[0] / valid_count + var = summary.sum_squares[0] - mean + if valid_count > 1: + var /= valid_count - 1 + sd = numpy.sqrt( var ) + + return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) ) + start = int(start) end = int(end) + + # The following seems not to work very well, for example it will only return one + # data point if the tile is 1280px wide. Not sure what the intent is. + # The first zoom level for BBI files is 640. If too much is requested, it will look at each block instead # of summaries. The calculation done is: zoom <> (end-start)/num_points/2. # Thus, the optimal number of points is (end-start)/num_points/2 = 640 # num_points = (end-start) / 1280 - num_points = (end-start) / 1280 - if num_points < 1: - num_points = end - start - else: - num_points = min(num_points, 500) + #num_points = (end-start) / 1280 + #if num_points < 1: + # num_points = end - start + #else: + # num_points = min(num_points, 500) - data = bbi.query(chrom, start, end, num_points) + # For now, we'll do 1000 data points by default However, the summaries + # don't seem to work when a summary pixel corresponds to less than one + # datapoint, so we prevent that. + # FIXME: need to switch over to using the full data at high levels of + # detail. + num_points = min( 1000, end - start ) + + summary = bbi.summarize( chrom, start, end, num_points ) f.close() + + result = [] + + if summary: + mean = summary.sum_data / summary.valid_count + + ## Standard deviation by bin, not yet used + ## var = summary.sum_squares - mean + ## var /= minimum( valid_count - 1, 1 ) + ## sd = sqrt( var ) - pos = start - step_size = (end - start) / num_points - result = [] - if data: - for dat_dict in data: - result.append( (pos, float_nan(dat_dict['mean']) ) ) + pos = start + step_size = (end - start) / num_points + + for i in range( num_points ): + result.append( (pos, float_nan( mean[i] ) ) ) pos += step_size return { 'data': result } diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/api/history_contents.py --- a/lib/galaxy/web/api/history_contents.py +++ b/lib/galaxy/web/api/history_contents.py @@ -50,7 +50,9 @@ """ content_id = id try: - content = self.get_history_dataset_association( trans, content_id, check_ownership=True, check_accessible=True ) + # get the history just for the access checks + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=False ) + content = self.get_history_dataset_association( trans, history, content_id, check_ownership=True, check_accessible=True ) except Exception, e: return str( e ) try: diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -6,6 +6,7 @@ from time import strftime from galaxy import config, tools, web, util from galaxy.util.hash_util import * +from galaxy.util.json import json_fix from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.workflow.modules import * @@ -19,9 +20,9 @@ from Cheetah.Template import Template - pkg_resources.require( 'elementtree' ) from elementtree import ElementTree, ElementInclude +from elementtree.ElementTree import Element log = logging.getLogger( __name__ ) @@ -233,16 +234,18 @@ else: error( "You are not allowed to access this dataset" ) return data - def get_history_dataset_association( self, trans, dataset_id, check_ownership=True, check_accessible=False ): + def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False ): """Get a HistoryDatasetAssociation from the database by id, verifying ownership.""" - hda = self.get_object( trans, id, 'HistoryDatasetAssociation', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) - self.security_check( trans, history, check_ownership=check_ownership, check_accessible=False ) # check accessibility here + self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) + hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) + if check_accessible: if trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): if hda.state == trans.model.Dataset.states.UPLOAD: error( "Please wait until this dataset finishes uploading before attempting to view it." ) else: error( "You are not allowed to access this dataset" ) + return hda def get_data( self, dataset, preview=True ): """ Gets a dataset's data. """ # Get data from file, truncating if necessary. @@ -1295,6 +1298,9 @@ group_list_grid = None quota_list_grid = None repository_list_grid = None + delete_operation = None + undelete_operation = None + purge_operation = None @web.expose @web.require_admin @@ -2214,6 +2220,13 @@ **kwd ) ) elif operation == "manage roles and groups": return self.manage_roles_and_groups_for_user( trans, **kwd ) + if trans.app.config.allow_user_deletion: + if self.delete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.delete_operation ) + if self.undelete_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.undelete_operation ) + if self.purge_operation not in self.user_list_grid.operations: + self.user_list_grid.operations.append( self.purge_operation ) # Render the list view return self.user_list_grid( trans, **kwd ) @web.expose diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -3,13 +3,15 @@ from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.tools.search import ToolBoxSearch -from galaxy.tools import json_fix +from galaxy.tools import ToolSection, json_fix +from galaxy.util import inflector import logging log = logging.getLogger( __name__ ) from galaxy.actions.admin import AdminActions from galaxy.web.params import QuotaParamParser from galaxy.exceptions import * +import galaxy.datatypes.registry class UserListGrid( grids.Grid ): class EmailColumn( grids.TextColumn ): @@ -93,11 +95,6 @@ allow_popup=False, url_args=dict( webapp="galaxy", action="reset_user_password" ) ) ] - #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if - # the setting is False - #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) - #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), @@ -403,7 +400,7 @@ def get_value( self, trans, grid, tool_shed_repository ): return tool_shed_repository.tool_shed # Grid definition - title = "Tool shed repositories" + title = "Installed tool shed repositories" model_class = model.ToolShedRepository template='/admin/tool_shed_repository/grid.mako' default_sort_key = "name" @@ -443,6 +440,9 @@ group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() repository_list_grid = RepositoryListGrid() + delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) + undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) + purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) @web.expose @web.require_admin @@ -807,28 +807,45 @@ status = kwd.get( 'status', 'done' ) tool_shed_url = kwd[ 'tool_shed_url' ] repo_info_dict = kwd[ 'repo_info_dict' ] + new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) + tool_panel_section = kwd.get( 'tool_panel_section', '' ) if kwd.get( 'select_tool_panel_section_button', False ): shed_tool_conf = kwd[ 'shed_tool_conf' ] # Get the tool path. for k, tool_path in trans.app.toolbox.shed_tool_confs.items(): if k == shed_tool_conf: break - if 'tool_panel_section' in kwd: - section_key = 'section_%s' % kwd[ 'tool_panel_section' ] - tool_section = trans.app.toolbox.tool_panel[ section_key ] + if new_tool_panel_section or tool_panel_section: + if new_tool_panel_section: + section_id = new_tool_panel_section.lower().replace( ' ', '_' ) + new_section_key = 'section_%s' % str( section_id ) + if new_section_key in trans.app.toolbox.tool_panel: + # Appending a tool to an existing section in trans.app.toolbox.tool_panel + log.debug( "Appending to tool panel section: %s" % new_tool_panel_section ) + tool_section = trans.app.toolbox.tool_panel[ new_section_key ] + else: + # Appending a new section to trans.app.toolbox.tool_panel + log.debug( "Loading new tool panel section: %s" % new_tool_panel_section ) + elem = Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section + elem.attrib[ 'id' ] = section_id + tool_section = ToolSection( elem ) + trans.app.toolbox.tool_panel[ new_section_key ] = tool_section + else: + section_key = 'section_%s' % tool_panel_section + tool_section = trans.app.toolbox.tool_panel[ section_key ] # Decode the encoded repo_info_dict param value. repo_info_dict = tool_shed_decode( repo_info_dict ) # Clone the repository to the configured location. current_working_dir = os.getcwd() + installed_repository_names = [] for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision = repo_info_tuple clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) if os.path.exists( clone_dir ): # Repository and revision has already been cloned. # TODO: implement the ability to re-install or revert an existing repository. - message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.<br/>' % \ - ( changeset_revision, name ) - status = 'error' + message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name ) else: os.makedirs( clone_dir ) log.debug( 'Cloning %s...' % repository_clone_url ) @@ -856,6 +873,10 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: + # Load data types required by tools. + # TODO: uncomment the following when we're ready... + #self.__load_datatypes( trans, repo_files_dir ) + # Load tools and tool data files required by them. sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. @@ -892,9 +913,7 @@ if trans.app.toolbox_search.enabled: # If search support for tools is enabled, index the new installed tools. trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) - message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \ - ( changeset_revision, name, tool_section.name ) - #return trans.show_ok_message( message ) + installed_repository_names.append( name ) else: tmp_stderr = open( tmp_name, 'rb' ) message += '%s<br/>' % tmp_stderr.read() @@ -905,6 +924,20 @@ message += '%s<br/>' % tmp_stderr.read() tmp_stderr.close() status = 'error' + if installed_repository_names: + installed_repository_names.sort() + num_repositories_installed = len( installed_repository_names ) + message += 'Installed %d %s and all tools were loaded into tool panel section <b>%s</b>:<br/>Installed repositories: ' % \ + ( num_repositories_installed, inflector.cond_plural( num_repositories_installed, 'repository' ), tool_section.name ) + for i, repo_name in enumerate( installed_repository_names ): + if i == len( installed_repository_names ) -1: + message += '%s.<br/>' % repo_name + else: + message += '%s, ' % repo_name + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tool_shed_repositories', + message=message, + status=status ) ) else: message = 'Choose the section in your tool panel to contain the installed tools.' status = 'error' @@ -921,6 +954,7 @@ shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, + new_tool_panel_section=new_tool_panel_section, message=message, status=status ) @web.expose @@ -1144,24 +1178,62 @@ error = tmp_stderr.read() tmp_stderr.close() log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + def __load_datatypes( self, trans, repo_files_dir ): + # Find datatypes_conf.xml if it exists. + datatypes_config = None + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + # Parse datatypes_config. + tree = ElementTree.parse( datatypes_config ) + root = tree.getroot() + ElementInclude.include( root ) + datatype_files = root.find( 'datatype_files' ) + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + relative_path = None + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + relative_path = os.path.join( root, name ) + break + relative_head, relative_tail = os.path.split( relative_path ) + # TODO: get the import_module by parsing the <registration><datatype> tags + if datatype_file_name.find( '.' ) > 0: + import_module = datatype_file_name.split( '.' )[ 0 ] + else: + import_module = datatype_file_name + try: + sys.path.insert( 0, relative_head ) + module = __import__( import_module ) + sys.path.pop( 0 ) + except Exception, e: + log.debug( "Execption importing datatypes code file included in installed repository: %s" % str( e ) ) + trans.app.datatypes_registry = galaxy.datatypes.registry.Registry( trans.app.config.root, datatypes_config ) def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): # The sample_files list contains all files whose name ends in .sample sample_files = [] + # Find all special .sample files first. + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs repository_tools_tups = [] for root, dirs, files in os.walk( repo_files_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... dirs.remove( '.hg' ) if 'hgrc' in files: - # Don't include hgrc files in commit. files.remove( 'hgrc' ) - # Find all special .sample files first. - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) for name in files: # Find all tool configs. if name.endswith( '.xml' ): diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py +++ b/lib/galaxy/web/controllers/async.py @@ -67,7 +67,7 @@ trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id ) galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) galaxy_url = params.get("GALAXY_URL",galaxy_url) - params = dict( url=URL, GALAXY_URL=galaxy_url ) + params = dict( URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext ) # Assume there is exactly one output file possible params[tool.outputs.keys()[0]] = data.id tool.execute( trans, incoming=params ) @@ -80,20 +80,20 @@ trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) - - # - # no data_id must be parameter submission - # - if not data_id and len(params)>3: - - if params.galaxyFileFormat == 'wig': + else: + # + # no data_id must be parameter submission + # + if params.data_type: + GALAXY_TYPE = params.data_type + elif params.galaxyFileFormat == 'wig': #this is an undocumented legacy special case GALAXY_TYPE = 'wig' else: - GALAXY_TYPE = params.GALAXY_TYPE or 'interval' + GALAXY_TYPE = params.GALAXY_TYPE or tool.outputs.values()[0].format - GALAXY_NAME = params.GALAXY_NAME or '%s query' % tool.name - GALAXY_INFO = params.GALAXY_INFO or params.galaxyDescription or '' - GALAXY_BUILD = params.GALAXY_BUILD or params.galaxyFreeze or 'hg17' + GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name + GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or '' + GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?' #data = datatypes.factory(ext=GALAXY_TYPE)() #data.ext = GALAXY_TYPE diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -806,7 +806,11 @@ #in case some display app wants all files to be in the same 'directory', #data can be forced to param, but not the other way (no filename for other direction) #get param name from url param name - action_param = display_link.get_param_name_by_url( action_param ) + try: + action_param = display_link.get_param_name_by_url( action_param ) + except ValueError, e: + log.debug( e ) + return paste.httpexceptions.HTTPNotFound( str( e ) ) value = display_link.get_param_value( action_param ) assert value, "An invalid parameter name was provided: %s" % action_param assert value.parameter.viewable, "This parameter is not viewable." diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1045,7 +1045,12 @@ status='error' ) ) json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] - return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) + job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) + # HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking" + job.add_parameter( 'link_data_only', to_json_string( kwd.get( 'link_data_only', 'copy_files' ) ) ) + trans.sa_session.add( job ) + trans.sa_session.flush() + return output def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() @@ -1855,7 +1860,7 @@ status=status ) @web.expose - def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_ids='', new_history_name='', **kwd ): + def import_datasets_to_histories( self, trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_id='', target_history_ids='', new_history_name='', **kwd ): # This method is called from one of the following places: # - a menu option for a library dataset ( ldda_ids is a single ldda id ) # - a menu option for a library folder ( folder_id has a value ) @@ -1870,7 +1875,6 @@ action = params.get( 'do_action', None ) user = trans.get_user() current_history = trans.get_history() - selected_history_id = params.get( 'selected_history_id', trans.security.encode_id( current_history.id ) ) if library_id: library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) else: @@ -1882,9 +1886,11 @@ ldda_ids = util.listify( ldda_ids ) if ldda_ids: ldda_ids = map( trans.security.decode_id, ldda_ids ) - target_history_ids = util.listify( target_history_ids ) if target_history_ids: - target_history_ids = [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ] + target_history_ids = util.listify( target_history_ids ) + target_history_ids = set( [ trans.security.decode_id( target_history_id ) for target_history_id in target_history_ids if target_history_id ] ) + elif target_history_id: + target_history_ids = [ trans.security.decode_id( target_history_id ) ] if params.get( 'import_datasets_to_histories_button', False ): invalid_datasets = 0 if not ldda_ids or not ( target_history_ids or new_history_name ): @@ -1965,7 +1971,7 @@ library=library, current_history=current_history, ldda_ids=ldda_ids, - selected_history_id=selected_history_id, + target_history_id=target_history_id, target_history_ids=target_history_ids, source_lddas=source_lddas, target_histories=target_histories, diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -13,7 +13,7 @@ from galaxy.web.framework import simplejson from galaxy.web.framework.helpers import time_ago, grids from galaxy.util.bunch import Bunch -from galaxy.datatypes.interval import Gff +from galaxy.datatypes.interval import Gff, Bed from galaxy.model import NoConverterException, ConverterDependencyException from galaxy.visualization.tracks.data_providers import * from galaxy.visualization.tracks.visual_analytics import get_tool_def, get_dataset_job @@ -246,6 +246,27 @@ "tool": get_tool_def( trans, dataset ) } return track + + @web.json + def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): + if hda_id: + hda_ldda = "hda" + dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True ) + elif ldda_id: + hda_ldda = "ldda" + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + rows = [] + if isinstance( dataset.datatype, Bed ): + data = RawBedDataProvider( original_dataset=dataset ).get_iterator() + for i, line in enumerate( data ): + if ( i > 500 ): break + fields = line.split() + location = name = "%s:%s-%s" % ( fields[0], fields[1], fields[2] ) + if len( fields ) > 3: + name = fields[4] + rows.append( [location, name] ) + return { 'data': rows } + @web.expose @web.require_login() @@ -528,6 +549,7 @@ if not standalone_provider.has_data( chrom ): return messages.NO_DATA valid_chroms = standalone_provider.valid_chroms() + # Have data if we get here return { "status": messages.DATA, "valid_chroms": valid_chroms } @@ -1041,4 +1063,4 @@ return_message = message elif return_message == None and message == messages.PENDING: return_message = message - return return_message \ No newline at end of file + return return_message diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -753,7 +753,7 @@ password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) ok = True - if not webapp == 'galaxy' and not is_admin: + if not is_admin: # If the current user is changing their own password, validate their current password current = kwd.get( 'current', '' ) if not trans.user.check_password( current ): @@ -768,10 +768,17 @@ else: # Save new password user.set_password_cleartext( password ) + # Invalidate all other sessions + for other_galaxy_session in trans.sa_session.query( trans.app.model.GalaxySession ) \ + .filter( and_( trans.app.model.GalaxySession.table.c.user_id==trans.user.id, + trans.app.model.GalaxySession.table.c.is_valid==True, + trans.app.model.GalaxySession.table.c.id!=trans.galaxy_session.id ) ): + other_galaxy_session.is_valid = False + trans.sa_session.add( other_galaxy_session ) trans.sa_session.add( user ) trans.sa_session.flush() trans.log_event( "User change password" ) - message = 'The password has been changed.' + message = 'The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).' elif user and params.get( 'edit_user_info_button', False ): # Edit user information - webapp MUST BE 'galaxy' user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -149,7 +149,8 @@ # Legacy issue: all shared workflows must have slugs. slug_set = False for workflow_assoc in shared_by_others: - slug_set = self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ) + if self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ): + slug_set = True if slug_set: trans.sa_session.flush() @@ -1115,10 +1116,10 @@ workflow_name = tool_shed_decode( workflow_name ) # The following parameters will have a value only if the import originated # from a tool shed repository installed locally. - local_file = kwd.get( 'local_file', '' ) + installed_repository_file = kwd.get( 'installed_repository_file', '' ) repository_id = kwd.get( 'repository_id', '' ) - if local_file and not import_button: - workflow_file = open( local_file, 'rb' ) + if installed_repository_file and not import_button: + workflow_file = open( installed_repository_file, 'rb' ) workflow_text = workflow_file.read() workflow_file.close() import_button = True @@ -1197,27 +1198,26 @@ if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp ) + if missing_tool_tups: + url += '&tool_id=' for missing_tool_tup in missing_tool_tups: missing_tool_id = missing_tool_tup[0] - url += '&tool_id=%s' % missing_tool_id + url += '%s,' % missing_tool_id message += '<a href="%s">%s</a><br/>' % ( url, shed_name ) status = 'error' - if local_file or tool_shed_url: + if installed_repository_file or tool_shed_url: # Another Galaxy panels Hack: The request did not originate from the Galaxy # workflow view, so we don't need to render the Galaxy panels. - return trans.response.send_redirect( web.url_for( controller='admin', - action='center', - webapp='galaxy', - message=message, - status=status ) ) + action = 'center' else: # Another Galaxy panels hack: The request originated from the Galaxy # workflow view, so we need to render the Galaxy panels. - return trans.response.send_redirect( web.url_for( controller='admin', - action='index', - webapp='galaxy', - message=message, - status=status ) ) + action = 'index' + return trans.response.send_redirect( web.url_for( controller='admin', + action=action, + webapp='galaxy', + message=message, + status=status ) ) else: # TODO: Figure out what to do here... pass @@ -1228,7 +1228,7 @@ url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) return trans.response.send_redirect( url ) - elif local_file: + elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository. message = "Workflow <b>%s</b> imported successfully." % workflow.name return trans.response.send_redirect( web.url_for( controller='admin', diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -61,6 +61,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -26,6 +26,8 @@ Change description: ${description} +${content_alert_str} + ----------------------------------------------------------------------------- This change alert was sent from the Galaxy tool shed hosted on the server "${host}" @@ -124,34 +126,6 @@ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() -def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): - """ - Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything in the database. - """ - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( exported_workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] - return metadata_dict -def new_workflow_metadata_required( trans, id, metadata_dict ): - """ - Currently everything about an exported workflow except the name is hard-coded, so there's - no real way to differentiate versions of exported workflows. If this changes at some future - time, this method should be enhanced accordingly. - """ - if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - if repository_metadata.metadata: - # The repository has metadata, so update the workflows value - no new record is needed. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table - # record is not needed. - return False def generate_clone_url( trans, repository_id ): repository = get_repository( trans, repository_id ) protocol, base = trans.request.base.split( '://' ) @@ -214,7 +188,8 @@ copy_sample_loc_file( trans, sample_file ) options.index_file = index_tail options.missing_index_file = None - options.tool_data_table.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None sample_found = True break if not sample_found: @@ -312,6 +287,62 @@ # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False +def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied + to the received exported_workflow_dict. Store everything in the database. + """ + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( exported_workflow_dict ) + else: + metadata_dict[ 'workflows' ] = [ exported_workflow_dict ] + return metadata_dict +def new_workflow_metadata_required( trans, id, metadata_dict ): + """ + Currently everything about an exported workflow except the name is hard-coded, so there's + no real way to differentiate versions of exported workflows. If this changes at some future + time, this method should be enhanced accordingly. + """ + if 'workflows' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + if repository_metadata.metadata: + # The repository has metadata, so update the workflows value - no new record is needed. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table + # record is not needed. + return False +def generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied + to the received datatypes_config. + """ + # Parse datatypes_config. + tree = ElementTree.parse( datatypes_config ) + root = tree.getroot() + ElementInclude.include( root ) + repository_datatype_code_files = [] + datatype_files = root.find( 'datatype_files' ) + if datatype_files: + for elem in datatype_files.findall( 'datatype_file' ): + name = elem.get( 'name', None ) + repository_datatype_code_files.append( name ) + metadata_dict[ 'datatype_files' ] = repository_datatype_code_files + datatypes = [] + registration = root.find( 'registration' ) + if registration: + for elem in registration.findall( 'datatype' ): + extension = elem.get( 'extension', None ) + dtype = elem.get( 'type', None ) + mimetype = elem.get( 'mimetype', None ) + datatypes.append( dict( extension=extension, + dtype=dtype, + mimetype=mimetype ) ) + metadata_dict[ 'datatypes' ] = datatypes + return metadata_dict def set_repository_metadata( trans, id, changeset_revision, **kwd ): """Set repository metadata""" message = '' @@ -321,37 +352,47 @@ repo = hg.repository( get_configured_ui(), repo_dir ) invalid_files = [] sample_files = [] + datatypes_config = None ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} if changeset_revision == repository.tip: + # Find datatypes_conf.xml if it exists. for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - # Find all special .sample files first. + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( trans, id, changeset_revision, datatypes_config, metadata_dict ) + # Find all special .sample files. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + # Find all tool configs and exported workflows. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) for name in files: # Find all tool configs. - if name.endswith( '.xml' ): + if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) try: - full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) + valid = True except Exception, e: + valid = False invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -370,11 +411,13 @@ # Find all special .sample files first. for filename in ctx: if filename.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, filename ) ) ) + sample_files.append( os.path.abspath( filename ) ) # Get all tool config file names from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml for filename in ctx: - # Find all tool configs - should not have to update metadata for workflows for now. + # Find all tool configs - we do not have to update metadata for workflows or datatypes in anything + # but repository tips (handled above) since at the time this code was written, no workflows or + # dataytpes_conf.xml files exist in tool shed repositories, so they can only be added in future tips. if filename.endswith( '.xml' ): fctx = ctx[ filename ] # Write the contents of the old tool config to a temporary file. @@ -386,17 +429,19 @@ fh.close() try: tool = load_tool( trans, tmp_filename ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename - # here is the relative path to the config file within the change set context, something - # like filtering.xml, but when the change set was the repository tip, the value was - # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break - # anything, but may result in a bit of confusion when maintaining the code / data over time. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + valid = True except Exception, e: - invalid_files.append( ( name, str( e ) ) ) + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) try: os.unlink( tmp_filename ) except: @@ -481,7 +526,7 @@ def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository ): +def handle_email_alerts( trans, repository, content_alert_str='' ): repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server @@ -502,14 +547,25 @@ username = ctx.user().split()[0] except: username = ctx.user() - # Build the email message + # We'll use 2 template bodies because we only want to send content + # alerts to tool shed admin users. + admin_body = string.Template( email_alert_template ) \ + .safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) body = string.Template( email_alert_template ) \ .safe_substitute( host=trans.request.host, repository_name=repository.name, revision='%s:%s' %( str( ctx.rev() ), ctx ), display_date=display_date, description=ctx.description(), - username=username ) + username=username, + content_alert_str='' ) + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) frm = email_from subject = "Galaxy tool shed repository update alert" email_alerts = from_json_string( repository.email_alerts ) @@ -517,9 +573,23 @@ to = email.strip() # Send it try: - util.send_mail( frm, to, subject, body, trans.app.config ) + if to in admin_users: + util.send_mail( frm, to, subject, admin_body, trans.app.config ) + else: + util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def check_file_contents( trans ): + # See if any admin users have chosen to receive email alerts when a repository is updated. + # If so, the file contents of the update must be checked for inappropriate content. + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.email_alerts != None ): + email_alerts = from_json_string( repository.email_alerts ) + for user_email in email_alerts: + if user_email in admin_users: + return True + return False def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # Make a copy of a repository's files for browsing, remove from disk all files that # are not tracked, and commit all added, modified or removed files that have not yet @@ -528,12 +598,10 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) - repo.ui.pushbuffer() - commands.status( repo.ui, repo, all=True ) - status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) - # status_and_file_names looks something like: - # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] - # The codes used to show the status of files are: + files_to_remove_from_disk = [] + files_to_commit = [] + # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. + # The codes used to show the status of files are as follows. # M = modified # A = added # R = removed @@ -541,37 +609,50 @@ # ! = deleted, but still tracked # ? = not tracked # I = ignored - files_to_remove_from_disk = [] - files_to_commit = [] - for status_and_file_name in status_and_file_names: - if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): - files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): - files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - for full_path in files_to_remove_from_disk: - # We'll remove all files that are not tracked or ignored. - if os.path.isdir( full_path ): - try: - os.rmdir( full_path ) - except OSError, e: - # The directory is not empty - pass - elif os.path.isfile( full_path ): - os.remove( full_path ) - dir = os.path.split( full_path )[0] - try: - os.rmdir( dir ) - except OSError, e: - # The directory is not empty - pass + # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the + # following entry in the repository's hgrc file which was not required for some time, so we'll add it + # if it's missing. + # [extensions] + # hgext.purge= + lines = repo.opener( 'hgrc', 'rb' ).readlines() + if not '[extensions]\n' in lines: + # No extensions have been added at all, so just append to the file. + fp = repo.opener( 'hgrc', 'a' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=\n' ) + fp.close() + elif not 'hgext.purge=\n' in lines: + # The file includes and [extensions] section, but we need to add the + # purge extension. + fp = repo.opener( 'hgrc', 'wb' ) + for line in lines: + if line.startswith( '[extensions]' ): + fp.write( line ) + fp.write( 'hgext.purge=\n' ) + else: + fp.write( line ) + fp.close() + cmd = 'hg purge' + os.chdir( repo_dir ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() + os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg purge failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) if files_to_commit: if not commit_message: commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) + cmd = 'hg update > /dev/null 2>&1' os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) def load_tool( trans, config_file ): """ Load a single tool from the file named by `config_file` and return diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1,4 +1,4 @@ -import os, logging, urllib, ConfigParser, tempfile, shutil +import os, logging, tempfile, shutil from time import strftime from datetime import date, datetime from galaxy import util @@ -236,7 +236,7 @@ template='/webapps/community/repository/grid.mako' default_sort_key = "Repository.name" columns = [ - NameColumn( "Name", + NameColumn( "Repository name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id, webapp="community" ) ), @@ -588,17 +588,17 @@ match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) else: ok = False - if workflow_names: + elif workflow_names: if 'workflows' in metadata: workflows = metadata[ 'workflows' ] else: workflows = [] for workflow_dict in workflows: for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name=workflow_name ): + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return ok, match_tuples - def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name=None ): + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() return ( workflow_name == workflow_dict_workflow_name ) or \ ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) @@ -773,7 +773,7 @@ tool_guids = [] for filename in ctx: # Find all tool configs in this repository changeset_revision. - if filename.endswith( '.xml' ): + if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ): fctx = ctx[ filename ] # Write the contents of the old tool config to a temporary file. fh = tempfile.NamedTemporaryFile( 'w' ) @@ -784,11 +784,11 @@ fh.close() try: tool = load_tool( trans, tmp_filename ) - if tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + valid = True except: - # File must not be a valid tool config even though it has a .xml extension. - pass + valid = False + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) try: os.unlink( tmp_filename ) except: @@ -1001,20 +1001,25 @@ hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __add_hgweb_config_entry( self, trans, repository, repository_path ): - # Add an entry in the hgweb.config file for a new repository. - # An entry looks something like: + # Add an entry in the hgweb.config file for a new repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root - # Make a backup of the hgweb.config file since we're going to be changing it. - self.__make_hgweb_config_copy( trans, hgweb_config ) + if repository_path.startswith( './' ): + repository_path = repository_path.replace( './', '', 1 ) entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) + tmp_fd, tmp_fname = tempfile.mkstemp() if os.path.exists( hgweb_config ): - output = open( hgweb_config, 'a' ) + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + new_hgweb_config.write( line ) else: - output = open( hgweb_config, 'w' ) - output.write( '[paths]\n' ) - output.write( "%s\n" % entry ) - output.close() + new_hgweb_config = open( tmp_fname, 'wb' ) + new_hgweb_config.write( '[paths]\n' ) + new_hgweb_config.write( "%s\n" % entry ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): # Change an entry in the hgweb.config file for a repository. This only happens when # the owner changes the name of the repository. An entry looks something like: @@ -1024,7 +1029,6 @@ self.__make_hgweb_config_copy( trans, hgweb_config ) repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) - old_entry = "%s = %s" % ( old_lhs, repo_dir ) new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) tmp_fd, tmp_fname = tempfile.mkstemp() new_hgweb_config = open( tmp_fname, 'wb' ) @@ -1033,17 +1037,16 @@ new_hgweb_config.write( new_entry ) else: new_hgweb_config.write( line ) + new_hgweb_config.flush() shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path. - # Create a .hg/hgrc file that looks something like this: - # [web] - # allow_push = test - # name = convert_characters1 - # push_ssl = False # Since we support both http and https, we set push_ssl to False to override # the default (which is True) in the mercurial api. + # The hg purge extension purges all files and directories not being tracked by + # mercurial in the current repository. It'll remove unknown files and empty + # directories. This is used in the update_for_browsing() method. repo = hg.repository( get_configured_ui(), path=repository.repo_path ) fp = repo.opener( 'hgrc', 'wb' ) fp.write( '[paths]\n' ) @@ -1053,6 +1056,8 @@ fp.write( 'allow_push = %s\n' % repository.user.username ) fp.write( 'name = %s\n' % repository.name ) fp.write( 'push_ssl = false\n' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=' ) fp.close() @web.expose def browse_repository( self, trans, id, **kwd ): @@ -1145,7 +1150,7 @@ tip = repository.tip for selected_file in selected_files_to_delete: try: - commands.remove( repo.ui, repo, repo_file, force=True ) + commands.remove( repo.ui, repo, selected_file, force=True ) except Exception, e: # I never have a problem with commands.remove on a Mac, but in the test/production # tool shed environment, it throws an exception whenever I delete all files from a @@ -1306,7 +1311,7 @@ if params.get( 'edit_repository_button', False ): flush_needed = False # TODO: add a can_manage in the security agent. - if user != repository.user: + if user != repository.user or not trans.user_is_admin(): message = "You are not the owner of this repository, so you cannot manage it." status = error return trans.response.send_redirect( web.url_for( controller='repository', @@ -1315,6 +1320,12 @@ webapp='community', message=message, status=status ) ) + if description != repository.description: + repository.description = description + flush_needed = True + if long_description != repository.long_description: + repository.long_description = long_description + flush_needed = True if repo_name != repository.name: message = self.__validate_repository_name( repo_name, user ) if message: @@ -1323,12 +1334,6 @@ self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) repository.name = repo_name flush_needed = True - if description != repository.description: - repository.description = description - flush_needed = True - if long_description != repository.long_description: - repository.long_description = long_description - flush_needed = True if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1609,39 +1614,49 @@ status = params.get( 'status', 'done' ) webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + valid = True + if changeset_revision == repository.tip: + try: + tool = load_tool( trans, os.path.abspath( tool_config ) ) + except Exception, e: + tool = None + valid = False + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + else: + # Get the tool config file name from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + old_tool_config_file_name = tool_config.split( '/' )[ -1 ] + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None + for filename in ctx: + filename_head, filename_tail = os.path.split( filename ) + if filename_tail == old_tool_config_file_name: + fctx = ctx[ filename ] + break + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + except Exception, e: + tool = None + valid = False + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) try: - if changeset_revision == repository.tip: - # Get the tool config from the file system we use for browsing. - tool = load_tool( trans, os.path.abspath( tool_config ) ) - else: - # Get the tool config file name from the hgweb url, something like: - # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - fctx = None - for filename in ctx: - filename_head, filename_tail = os.path.split( filename ) - if filename_tail == old_tool_config_file_name: - fctx = ctx[ filename ] - break - if fctx: - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - tool = load_tool( trans, tmp_filename ) - try: - os.unlink( tmp_filename ) - except: - pass - else: - tool = None - tool_state = self.__new_state( trans ) - is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, @@ -1652,7 +1667,7 @@ message=message, status=status ) except Exception, e: - message = "Error loading tool: %s. Click <b>Reset metadata</b> to correct this error." % str( e ) + message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,4 +1,4 @@ -import sys, os, shutil, logging, tarfile, tempfile +import sys, os, shutil, logging, tarfile, tempfile, urllib from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes.checkers import * @@ -11,9 +11,6 @@ SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" CHUNK_SIZE = 2**20 # 1Mb -class UploadError( Exception ): - pass - class UploadController( BaseUIController ): @web.expose @web.require_login( 'upload', use_panels=True, webapp='community' ) @@ -32,20 +29,40 @@ remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = self.__get_upload_point( repository, **kwd ) - # Get the current repository tip. tip = repository.tip + file_data = params.get( 'file_data', '' ) + url = params.get( 'url', '' ) if params.get( 'upload_button', False ): current_working_dir = os.getcwd() - file_data = params.get( 'file_data', '' ) - if file_data == '': + if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error uploading file via http: %s' % str( e ) + status = 'error' + uploaded_file = None + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 elif file_data not in ( '', None ): uploaded_file = file_data.file uploaded_file_name = uploaded_file.name uploaded_file_filename = file_data.filename - isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file: isgzip = False isbz2 = False @@ -86,6 +103,13 @@ full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) + if check_contents and os.path.isfile( full_path ): + content_alert_str = self.__check_file_content( full_path ) + else: + content_alert_str = '' commands.add( repo.ui, repo, full_path ) try: commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) @@ -107,7 +131,7 @@ # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str=content_alert_str ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -146,6 +170,7 @@ selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, + url=url, commit_message=commit_message, uncompress_file=uncompress_file, remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, @@ -172,6 +197,7 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() + content_alert_str = '' if remove_repo_files_not_in_tar and not repository.is_new: # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. @@ -215,7 +241,13 @@ except OSError, e: # The directory is not empty pass + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) for filename_in_archive in filenames_in_archive: + # Check file content to ensure it is appropriate. + if check_contents and os.path.isfile( filename_in_archive ): + content_alert_str += self.__check_file_content( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample @@ -237,7 +269,7 @@ # exception. If this happens, we'll try the following. repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str ) return True, '', files_to_remove def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: @@ -314,4 +346,10 @@ message = "Uploaded archives cannot contain hgrc files." return False, message return True, '' - + def __check_file_content( self, file_path ): + message = '' + if check_html( file_path ): + message = 'The file "%s" contains HTML content.\n' % str( file_path ) + elif check_image( file_path ): + message = 'The file "%s" contains image content.\n' % str( file_path ) + return message diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/demo_sequencer/config.py --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -40,6 +40,7 @@ self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca lib/galaxy/webapps/reports/config.py --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -31,6 +31,8 @@ self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/reports" ), self.root ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") + self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca locale/zh/LC_MESSAGES/ginga.mo Binary file locale/zh/LC_MESSAGES/ginga.mo has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca locale/zh/LC_MESSAGES/ginga.po --- /dev/null +++ b/locale/zh/LC_MESSAGES/ginga.po @@ -0,0 +1,597 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER +# This file is distributed under the same license as the PACKAGE package. +# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: yinhe 1.0\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2011-10-15 13:58+0800\n" +"PO-Revision-Date: 2011-11-04 19:13+0900\n" +"Last-Translator: Hanfei Sun <hfsun.tju@gmail.com> Juan Wang <jinling8@gmail.com>\n" +"Language-Team: Chinese\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" + +#: +msgid "iso-8859-1" +msgstr "utf-8" + +#: +msgid "lang=\"en\"" +msgstr "lang=\"zh\"" + + +#: templates/base_panels.mako:5 +msgid "Galaxy" +msgstr "Galaxy" + +#: templates/history/options.mako:24 +msgid "Are you sure you want to delete the current history?" +msgstr "确认要删除当前的历史记录吗？" + + +#: templates/root/history.mako:38 +msgid "collapse all" +msgstr "全部收缩" + + +#: templates/root/index.mako:5 +msgid "Tools" +msgstr "工具" + + +#: tools/**.xml +msgid "Get Data" +msgstr "获取数据" + +msgid "Get ENCODE Data" +msgstr "获取ENCODE数据" + +msgid "ENCODE Tools" +msgstr "ENCODE工具" + +msgid "Lift-Over" +msgstr "版本转换" + + +msgid "Text Manipulation" +msgstr "文本操作" + +msgid "Filter and Sort" +msgstr "过滤和排序" + +msgid "Join, Subtract and Group" +msgstr "结合，差集与分组" + +msgid "Convert Formats" +msgstr "格式转换" + +msgid "Extract Features" +msgstr "特征提取" + +msgid "Fetch Sequences" +msgstr "获取序列" + +msgid "Fetch Alignments" +msgstr "获取比对上的序列" + +msgid "Get Genomic Scores" +msgstr "获得基因组分数" + +msgid "Operate on Genomic Intervals" +msgstr "基因组区间操作" + +msgid "Statistics" +msgstr "统计量" + +msgid "Graph/Display Data" +msgstr "图形／数据" + +msgid "Regional Variation" +msgstr "区域多态性" + +msgid "Evolution: HyPhy" +msgstr "进化: HyPhy" + +msgid "Taxonomy manipulation" +msgstr "分类处理" + +msgid "Solexa tools" +msgstr "Solexa工具" + +msgid "FASTA manipulation" +msgstr "FASTA处理" + +msgid "Short Read QC and Manipulation" +msgstr "短片段数据质量控制及处理" + +msgid "Short Read Mapping" +msgstr "短片段回贴" + + +#: templates/admin_main.mako:3 templates/admin_main.mako:8 +msgid "Galaxy Administration" +msgstr "Galaxy 管理" + +#: templates/admin_main.mako:17 +msgid "Admin password: " +msgstr "管理员密码: " + +#: templates/admin_main.mako:19 +msgid "Reload tool: " +msgstr "重新载入工具" + +#: templates/admin_main.mako:35 +msgid "Reload" +msgstr "重新载入" + +#: templates/dataset/edit_attributes.mako:2 +msgid "History Item Attributes" +msgstr "历史项目属性" + +#: templates/dataset/edit_attributes.mako:19 +msgid "Edit Attributes" +msgstr "编辑属性" + +#: templates/dataset/edit_attributes.mako:64 +msgid "" +"This will inspect the dataset and attempt to correct the above column values " +"if they are not accurate." +msgstr "数据集检查，若有错误，更正上述栏中的值。" + +#: templates/dataset/edit_attributes.mako:68 +msgid "" +"Required metadata values are missing. Some of these values may not be " +"editable by the user. Selecting \"Auto-detect\" will attempt to fix these " +"values." +msgstr "所需元数据值缺失。其中一些值可能无法被用户编辑。选择“自动检测”将修正这些值。" + +#: templates/dataset/edit_attributes.mako:78 +msgid "Convert to new format" +msgstr "转换成新格式" + +#: templates/dataset/edit_attributes.mako:84 +msgid "Convert to" +msgstr "转换" + +#: templates/dataset/edit_attributes.mako:95 +msgid "" +"This will create a new dataset with the contents of this dataset converted " +"to a new format." +msgstr "这将创建一个新的数据集，内容是转换后的数据集。" + +#: templates/dataset/edit_attributes.mako:111 +msgid "Change data type" +msgstr "改变数据类型" + +#: templates/dataset/edit_attributes.mako:117 +msgid "New Type" +msgstr "新类型" + +#: templates/dataset/edit_attributes.mako:124 +msgid "" +"This will change the datatype of the existing dataset but <i>not</i> modify " +"its contents. Use this if Galaxy has incorrectly guessed the type of your " +"dataset." +msgstr "这将改变已有数据集的数据类型，但是<i>不</i>改变其内容。当Galaxy不能正确判断你的数据类型时，设置该参数。" + +#: templates/dataset/edit_attributes.mako:137 +msgid "Copy History Item" +msgstr "复制历史记录项" + +#: templates/history/list.mako:3 +msgid "Saved Histories" +msgstr "保存的历史记录" + +#: templates/history/list.mako:19 +msgid "Stored Histories" +msgstr "存储的历史记录" + +#: templates/history/list.mako:21 templates/root/history.mako:239 +msgid "hide deleted" +msgstr "隐藏已删除" + +#: templates/history/list.mako:23 +msgid "show deleted" +msgstr "显示已删除" + +#: templates/history/list.mako:27 +msgid "Name" +msgstr "名称" + +#: templates/history/list.mako:27 +msgid "Size" +msgstr "大小" + +#: templates/history/list.mako:27 +msgid "Last modified" +msgstr "最后修改" + +#: templates/history/list.mako:27 +msgid "Actions" +msgstr "操作" + +#: templates/history/list.mako:45 +msgid "rename" +msgstr "重命名" + +#: templates/history/list.mako:46 +msgid "switch to" +msgstr "切换到" + +#: templates/history/list.mako:47 +msgid "delete" +msgstr "删除" + +#: templates/history/list.mako:49 +msgid "undelete" +msgstr "取消删除" + +#: templates/history/list.mako:55 +msgid "Action" +msgstr "操作" + +#: templates/history/list.mako:56 templates/history/options.mako:21 +msgid "Share" +msgstr "共享" + +#: templates/history/list.mako:56 templates/history/options.mako:15 +msgid "Rename" +msgstr "重命名" + +#: templates/history/list.mako:56 templates/history/options.mako:24 +msgid "Delete" +msgstr "删除" + +#: templates/history/list.mako:58 +msgid "Undelete" +msgstr "取消删除" + +#: templates/history/list.mako:65 +msgid "You have no stored histories" +msgstr "没有存储的历史记录" + +#: templates/history/options.mako:5 +msgid "History Options" +msgstr "历史记录选项" + +#: templates/history/options.mako:9 +msgid "You must be " +msgstr "你必须" + +#: templates/history/options.mako:9 +msgid "logged in" +msgstr "登录" + +#: templates/history/options.mako:9 +msgid " to store or switch histories." +msgstr "以存储或切换历史记录" + +#: templates/history/options.mako:15 +#, python-format +msgid " current history (stored as \"%s\")" +msgstr " 当前历史（以\"%s\"形式存储）" + +#: templates/history/options.mako:16 +msgid "List" +msgstr "列表" + +#: templates/history/options.mako:16 +msgid " previously stored histories" +msgstr " 以前存储的历史记录" + +#: templates/history/options.mako:18 +msgid "Create" +msgstr "创建" + +#: templates/history/options.mako:18 +msgid " a new empty history" +msgstr " 一个新的空历史记录" + +#: templates/history/options.mako:20 +msgid "Construct workflow" +msgstr "构建工作流程" + +#: templates/history/options.mako:20 +msgid " from the current history" +msgstr " 来源于当前历史" + +#: templates/history/options.mako:21 templates/history/options.mako:24 +msgid " current history" +msgstr " 当前历史" + +#: templates/history/options.mako:23 +msgid "Show deleted" +msgstr "显示已删除" + +#: templates/history/options.mako:23 +msgid " datasets in history" +msgstr " 历史中的数据集" + +#: templates/history/rename.mako:3 templates/history/rename.mako:6 +msgid "Rename History" +msgstr "重命名历史" + + +msgid "Rename Histories" +msgstr "重命名历史记录" + +msgid "Perform Action" +msgstr "运行操作" + +msgid "Submit" +msgstr "提交" + + + +#: templates/history/rename.mako:10 +msgid "Current Name" +msgstr "当前名称" + +#: templates/history/rename.mako:10 +msgid "New Name" +msgstr "新名称" + +#: templates/history/share.mako:3 +msgid "Share histories" +msgstr "共享历史记录" + +#: templates/history/share.mako:6 +msgid "Share Histories" +msgstr "共享历史记录" + +#: templates/history/share.mako:9 +msgid "History Name:" +msgstr "历史名称" + +#: templates/history/share.mako:9 +msgid "Number of Datasets:" +msgstr "数据集数量" + +#: templates/history/share.mako:9 +msgid "Share Link" +msgstr "共享链接" + +#: templates/history/share.mako:15 +msgid "This history contains no data." +msgstr "这项历史中没有数据" + +#: templates/history/share.mako:21 +msgid "copy link to share" +msgstr "复制链接以共享" + +#: templates/history/share.mako:24 +msgid "Email of User to share with:" +msgstr "发送到这些Email地址进行分享" + +#: templates/root/history.mako:7 +msgid "Galaxy History" +msgstr "Galaxy 历史" + +#: templates/root/history.mako:237 +msgid "refresh" +msgstr "刷新" + +#: templates/root/history.mako:245 +msgid "You are currently viewing a deleted history!" +msgstr "正在查看已删除的历史" + +#: templates/root/history.mako:289 +msgid "Your history is empty. Click 'Get Data' on the left pane to start" +msgstr "历史已空，请单击左边窗格中‘获取数据’" + +#: templates/root/history_common.mako:41 +msgid "Job is waiting to run" +msgstr "等待运行的进程" + +#: templates/root/history_common.mako:43 +msgid "Job is currently running" +msgstr "正在运行的进程" + +#: templates/root/history_common.mako:46 +msgid "An error occurred running this job: " +msgstr "进程运行时出错 " + +#: templates/root/history_common.mako:47 +msgid "report this error" +msgstr "报告错误" + +#: templates/root/history_common.mako:54 +msgid "No data: " +msgstr "没有数据： " + +#: templates/root/history_common.mako:58 +msgid "format: " +msgstr "格式： " + +#: templates/root/history_common.mako:59 +msgid "database: " +msgstr "数据库： " + +#: templates/root/history_common.mako:66 templates/root/masthead.mako:20 +msgid "Info: " +msgstr "信息： " + +#: templates/root/history_common.mako:85 +#, python-format +msgid "Error: unknown dataset state \"%s\"." +msgstr "错误：未知的数据集状态 \"%s\"。" + + +msgid "Options" +msgstr "选项" + +msgid "History" +msgstr "历史" + +#: templates/root/masthead.mako:20 +msgid "report bugs" +msgstr "错误报告" + +#: templates/root/masthead.mako:21 +msgid "wiki" +msgstr "wiki" + +#: templates/root/masthead.mako:22 +msgid "screencasts" +msgstr "演示视频" + + +#: templates/root/masthead.mako:23 +msgid "blog" +msgstr "博客" + +#: templates/root/masthead.mako:31 +#, python-format +msgid "Logged in as %s: " +msgstr "以%s的身份登录: " + +#: templates/root/masthead.mako:31 +msgid "manage" +msgstr "管理" + +#: templates/root/masthead.mako:32 +msgid "logout" +msgstr "注销" + +#: templates/root/masthead.mako:34 +msgid "Account: " +msgstr "帐户: " + +#: templates/root/masthead.mako:34 +msgid "create" +msgstr "创建" + +#: templates/root/masthead.mako:35 +msgid "login" +msgstr "登录" + +#: templates/root/tool_menu.mako:52 +msgid "Galaxy Tools" +msgstr "Galaxy 工具" + +#: templates/root/tool_menu.mako:129 +msgid "Workflow" +msgstr "工作流程" + +#: templates/root/tool_menu.mako:134 +msgid "Manage" +msgstr "管理" + +#: templates/root/tool_menu.mako:134 +msgid "workflows" +msgstr "工作流程" + +#: templates/user/index.mako:2 templates/user/index.mako:4 +msgid "Account settings" +msgstr "帐户设置" + +#: templates/user/index.mako:7 +#, python-format +msgid "You are currently logged in as %s." +msgstr "当前以%s的身份登录" + +#: templates/user/index.mako:9 +msgid "Change your password" +msgstr "修改密码" + +#: templates/user/index.mako:10 +msgid "Update your email address" +msgstr "更新电子邮件地址" + +#: templates/user/index.mako:11 +msgid "Logout" +msgstr "注销" + +#: templates/user/index.mako:16 +msgid "Login" +msgstr "登录" + +#: templates/user/index.mako:17 +msgid "Create new account" +msgstr "创建新帐户" + +msgid "Show Tool Search" +msgstr "显示工具搜索" + +msgid "Analyze Data" +msgstr "分析数据" + +msgid "analysis" +msgstr "分析" + +msgid "History Lists" +msgstr "历史记录清单" + +msgid "Histories Shared with Me" +msgstr "共享的数据" + +msgid "Current History" +msgstr "当前历史记录" + +msgid "Create New" +msgstr "创建" + +msgid "Clone" +msgstr "复制" + +msgid "Share or Publish" +msgstr "共享或发布" + +msgid "Extract Workflow" +msgstr "提取工作流程" + +msgid "Dataset Security" +msgstr "数据安全性" + + +msgid "Show Deleted Datasets" +msgstr "显示已删除数据" + +msgid "Show Hidden Datasets" +msgstr "显示隐藏数据" + +msgid "Show Structure" +msgstr "显示结构" + +msgid "Export to File" +msgstr "导出为文件" + +msgid "Other Actions" +msgstr "其他" + +msgid "Import from File" +msgstr "导入文件" + +msgid "Shared Data" +msgstr "数据共享" + +msgid "Data Libraries" +msgstr "数据仓库" + +msgid "Published Histories" +msgstr "已发布的历史记录" + +msgid "Published Workflows" +msgstr "已发布的工作流程" + +msgid "Published Pages" +msgstr "已发布的页面" + +msgid "Help" +msgstr "帮助" + +msgid "Email comments, bug reports, or suggestions" +msgstr "发邮件进行意见反馈或错误报告" + + +msgid "User" +msgstr "用户" + + +msgid "Register" +msgstr "注册" \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca locale/zh/LC_MESSAGES/tools.mo Binary file locale/zh/LC_MESSAGES/tools.mo has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca locale/zh/LC_MESSAGES/tools.po --- /dev/null +++ b/locale/zh/LC_MESSAGES/tools.po @@ -0,0 +1,84 @@ +# Japanese translations for PROJECT. +# Copyright (C) 2009 ORGANIZATION +# This file is distributed under the same license as the PROJECT project. +# FIRST AUTHOR <EMAIL@ADDRESS>, 2009. +# +msgid "" +msgstr "" +"Project-Id-Version: PROJECT VERSION\n" +"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n" +"POT-Creation-Date: 2009-03-17 04:06-0400\n" +"PO-Revision-Date: 2009-03-17 04:06-0400\n" +"Last-Translator: Hanfei Sun <hfsun.tju@gmail.com>\n" +"Language-Team: zh <hfsun.tju@gmail.com>\n" +"Plural-Forms: nplurals=1; plural=0\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=utf-8\n" +"Content-Transfer-Encoding: 8bit\n" +"Generated-By: Babel 0.9.4\n" + +msgid "Get Data" +msgstr "获取数据" + +msgid "Get ENCODE Data" +msgstr "" + +msgid "ENCODE Tools" +msgstr "" + +msgid "Lift-Over" +msgstr "" + +msgid "Text Manipulation" +msgstr "" + +msgid "Filter and Sort" +msgstr "" + +msgid "Join, Subtract and Group" +msgstr "" + +msgid "Convert Formats" +msgstr "" + +msgid "Extract Features" +msgstr "" + +msgid "Fetch Sequences" +msgstr "" + +msgid "Fetch Alignments" +msgstr "" + +msgid "Get Genomic Scores" +msgstr "" + +msgid "Operate on Genomic Intervals" +msgstr "" + +msgid "Statistics" +msgstr "" + +msgid "Graph/Display Data" +msgstr "" + +msgid "Regional Variation" +msgstr "" + +msgid "Evolution: HyPhy" +msgstr "" + +msgid "Taxonomy manipulation" +msgstr "" + +msgid "Solexa tools" +msgstr "" + +msgid "FASTA manipulation" +msgstr "" + +msgid "Short Read QC and Manipulation" +msgstr "" + +msgid "Short Read Mapping" +msgstr "" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca run.sh --- a/run.sh +++ b/run.sh @@ -15,6 +15,7 @@ tool_sheds_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample tool-data/*.sample static/welcome.html.sample " diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/images/fugue/chevron-expand-bw.png Binary file static/images/fugue/chevron-expand-bw.png has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/images/fugue/toggle-bw.png Binary file static/images/fugue/toggle-bw.png has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/images/fugue/toggle-expand-bw.png Binary file static/images/fugue/toggle-expand-bw.png has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -231,6 +231,10 @@ padding: 3px 0 0 1em; } +.form-row .help { + color: #666; +} + select, input, textarea { font: inherit; } @@ -865,10 +869,6 @@ -sprite-group: fugue; -sprite-image: fugue/toggle.png; } -.icon-button.toggle-contract { - -sprite-group: fugue; - -sprite-image: fugue/toggle.png; -} .icon-button.arrow-circle { -sprite-group: fugue; -sprite-image: fugue/arrow-circle.png; @@ -905,6 +905,14 @@ -sprite-group: fugue; -sprite-image: fugue/plus-circle.png; } +.icon-button.plus-button { + -sprite-group: fugue; + -sprite-image: fugue/plus-button.png; +} +.icon-button.gear { + -sprite-group: fugue; + -sprite-image: fugue/gear.png; +} .tipsy { padding: 5px; diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -43,6 +43,7 @@ div.form-row-input{float:left;} div.form-row-input label{font-weight:normal;display:inline;} div.form-row-error-message{width:300px;float:left;color:red;font-weight:bold;padding:3px 0 0 1em;} +.form-row .help{color:#666;} select,input,textarea{font:inherit;} select,textarea,input[type="text"],input[type="file"],input[type="password"]{-webkit-box-sizing:border-box;max-width:300px;} .errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:10px;padding-left:52px;min-height:32px;border:1px solid #AA6666;background-color:#FFCCCC;background-image:url(error_message_icon.png);background-repeat:no-repeat;background-position:10px 10px;} @@ -150,9 +151,10 @@ .icon-button.tag{background:url(fugue.png) no-repeat 0px -0px;} .icon-button.tags{background:url(fugue.png) no-repeat 0px -26px;} .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} -.icon-button.toggle-expand{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle{background:url(fugue.png) no-repeat 0px -104px;} -.icon-button.toggle-contract{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;} +.icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;} +.icon-button.toggle{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} +.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -104px;} .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} @@ -162,6 +164,8 @@ .icon-button.vis-chart{background:url(fugue.png) no-repeat 0px -286px;} .icon-button.go-to-full-screen{background:url(fugue.png) no-repeat 0px -312px;} .icon-button.import{background:url(fugue.png) no-repeat 0px -338px;} +.icon-button.plus-button{background:url(fugue.png) no-repeat 0px -364px;} +.icon-button.gear{background:url(fugue.png) no-repeat 0px -390px;} .tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} .tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} .tipsy-north{background-position:top center;} @@ -170,7 +174,7 @@ .tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} -.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} +.text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/blue/fugue.png Binary file static/june_2007_style/blue/fugue.png has changed diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css +++ b/static/june_2007_style/blue/panel_layout.css @@ -23,9 +23,11 @@ .panel-header-button:hover{color:black;background-color:#ccc;} .panel-header-button:active{color:white;background-color:#aaaaaa;} #overlay{position:fixed;top:0;left:0;width:100%;height:100%;z-index:20000;} +#overlay.modal #overlay-background{background:rgba(0,0,0,0.5);} .dialog-box-container{position:relative;margin-top:80px;margin-right:auto;margin-left:auto;} .dialog-box-wrapper{position:relative;padding:1em;background-color:rgba(0,0,0,0.5);-moz-border-radius:1em;-webkit-border-radius:1em;} .dialog-box{border:solid #999 1px;background:white;z-index:80000;} +#overlay.modal .dialog-box .body{min-width:600px;} .dialog-box .body{padding:5px;overflow:auto;max-height:500px;min-width:300px;} .dialog-box .buttons{padding:5px;} .panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;color:#303030;padding:0px;padding-left:26px;background-color:#FFCCCC;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%;} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -3,30 +3,9 @@ .content{font:10px verdana;} .nav-controls{text-align:center;padding:1px 0;} .nav-controls input{margin:0 5px;} -.menu-button{padding: 0px 4px 0px 4px;} #zoom-in,#zoom-out{display:inline-block;height:16px;width:16px;margin-bottom:-3px;cursor:pointer;} #zoom-out{background:transparent url(../images/fugue/magnifier-zoom-out.png) center center no-repeat;} #zoom-in{margin-left:10px;background:transparent url(../images/fugue/magnifier-zoom.png) center center no-repeat;} -.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} -.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} -.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} -.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} -.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} -.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} -.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} -.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} -.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} -.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} -#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} -#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} -#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} -#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;} -#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} -#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} -#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} -#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;} -#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;} -#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;} .nav-input{font-size:12px;width:30em;z-index:1000;} .location{display:inline-block;width:15em;margin:0 10px;} .draghandle{margin-top:2px;cursor:move;float:left;background:transparent url(../images/visualization/draggable_horizontal.png) center center no-repeat;width:10px;height:12px;} @@ -65,16 +44,41 @@ input{font:10px verdana;} .dynamic-tool,.filters{margin-left:0.25em;padding-bottom:0.5em;} .dynamic-tool{width:410px;} -.filters>.sliders,.display-controls{float:left;margin:1em;} +.filters > .sliders,.display-controls{float:left;margin:1em;} .sliders{width:410px;} -.display-controls{border-left:solid 2px #DDDDDD;padding-left:1em} -.filter-row{margin-top:0.4em;} +.display-controls{border-left:solid 2px #DDDDDD;padding-left:1em +} +.filter-row { + margin-top:0.4em;} .slider-row{margin-left:1em;} .elt-label{float:left;font-weight:bold;margin-right:1em;} .slider{float:right;width:200px;position:relative;} .tool-name{font-size:110%;font-weight:bold;} .param-row{margin-top:0.2em;margin-left:1em;} .param-label{float:left;font-weight:bold;padding-top:0.2em;} +.menu-button{margin:0px 4px 0px 4px;} +.chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} +.chevron-expand:hover{background:transparent url(../images/fugue/chevron-expand.png) no-repeat;} +.settings-icon{background:transparent url(../images/fugue/gear-bw.png) no-repeat;} +.settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} +.overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} +.overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} +.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} +.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} +.filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} +.filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} +.remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} +.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#close-icon{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} +#close-icon:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +#add-tracks-icon{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} +#add-tracks-icon:hover{background:transparent url(../images/fugue/plus-button.png) no-repeat;} +#add-group-icon{background:transparent url(../images/fugue/block--plus-bw.png) no-repeat;} +#add-group-icon:hover{background:transparent url(../images/fugue/block--plus.png) no-repeat;} +#bookmarks-icon{background:transparent url(../images/fugue/bookmarks-bw.png) no-repeat;} +#bookmarks-icon:hover{background:transparent url(../images/fugue/bookmarks.png) no-repeat;} +#save-icon{background:transparent url(../images/fugue/disk--arrow-bw.png) no-repeat;} +#save-icon:hover{background:transparent url(../images/fugue/disk--arrow.png) no-repeat;} .child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;} .track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;} .bookmark{background:white;border:solid #999 1px;border-right:none;margin:0.5em;margin-right:0;padding:0.5em;} @@ -85,4 +89,5 @@ .icon.more-across{background:url('../images/fugue/arrow-transition-bw.png') no-repeat 0px 0px;} .intro{padding:1em;} .intro > .action-button{background-color:#CCC;padding:1em;} -.feature-popup{background-color:#DDD;position:absolute;z-index:1000} +.feature-popup{position:absolute;z-index:1000;padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);background-position:top center;} +.feature-popup-inner{padding:5px 8px 4px 8px;background-color:black;color:white;} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl +++ b/static/june_2007_style/panel_layout.css.tmpl @@ -161,6 +161,10 @@ z-index: 20000; } +#overlay.modal #overlay-background { + background: rgba(0,0,0,0.5); +} + .dialog-box-container { position: relative; margin-top: 80px; @@ -182,6 +186,10 @@ z-index: 80000; } +#overlay.modal .dialog-box .body { + min-width: 600px; +} + .dialog-box .body { padding: 5px; overflow: auto; diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -295,7 +295,13 @@ padding-top: 0.2em; } .menu-button { - padding: 0px 4px 0px 4px; + margin: 0px 4px 0px 4px; +} +.chevron-expand { + background: transparent url(../images/fugue/chevron-expand-bw.png) no-repeat; +} +.chevron-expand:hover { + background:transparent url(../images/fugue/chevron-expand.png) no-repeat; } .settings-icon { background: transparent url(../images/fugue/gear-bw.png) no-repeat; @@ -405,8 +411,19 @@ background-color: #CCC; padding: 1em; } -.feature-popup{ - background-color: #DDD; + +.feature-popup { position: absolute; - z-index: 1000 + z-index: 1000; + padding: 5px; + font-size: 10px; + filter: alpha(opacity=80); + background-repeat: no-repeat; + background-image: url(../images/tipsy.gif); + background-position: top center; } +.feature-popup-inner { + padding: 5px 8px 4px 8px; + background-color: black; + color: white; +} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -163,13 +163,23 @@ // Modal dialog boxes function hide_modal() { - $(".dialog-box-container" ).fadeOut( function() { + $(".dialog-box-container" ).hide( 0, function() { $("#overlay").hide(); + $("#overlay").removeClass( "modal" ); $( ".dialog-box" ).find( ".body" ).children().remove(); } ); }; -function show_modal( title, body, buttons, extra_buttons, init_fn ) { +function show_modal() { + $("#overlay").addClass( "modal" ); + _show_modal.apply( this, arguments ); +} + +function show_message() { + _show_modal.apply( this, arguments ); +} + +function _show_modal( title, body, buttons, extra_buttons, init_fn ) { if ( title ) { $( ".dialog-box" ).find( ".title" ).html( title ); $( ".dialog-box" ).find( ".unified-panel-header" ).show(); @@ -205,7 +215,7 @@ $( ".dialog-box" ).find( ".body" ).html( body ); if ( ! $(".dialog-box-container").is( ":visible" ) ) { $("#overlay").show(); - $(".dialog-box-container").fadeIn(); + $(".dialog-box-container").show(); } // Fix min-width so that modal cannot shrink considerably if // new content is loaded. diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").fadeOut(function(){$("#overlay").hide();$(".dialog-box").find(".body").children().remove()})}function show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file +function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}var MIN_PANEL_WIDTH=100,MAX_PANEL_WIDTH=1000;function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var a=function(){if(g){$(e).removeClass("hover");$(e).animate({left:f},"fast");$(h).css("left",-f).show().animate({left:0},"fast",function(){d(f);$(e).removeClass("hidden")});g=false}else{f=$(e).position().left;$(c).css("left",$(e).innerWidth());if(document.recalc){document.recalc()}$(e).removeClass("hover");$(h).animate({left:-f},"fast");$(e).animate({left:-1},"fast",function(){$(this).addClass("hidden")});g=true}};$(e).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(i,j){x=j.offsetX;x=Math.min(MAX_PANEL_WIDTH,Math.max(MIN_PANEL_WIDTH,x));if(g){$(h).css("left",0);$(e).removeClass("hidden");g=false}d(x)}).bind("dragclickonly",function(){a()}).find("div").show();var b=function(i){if((g&&i=="show")||(!g&&i=="hide")){a()}};return{force_panel:b}}function make_right_panel(a,e,h){var j=false,g=false,c=null;var d=function(k){$(a).css("width",k);$(e).css("right",k+9);$(h).css("right",k).css("left","");if(document.recalc){document.recalc()}};var i=function(){if(j){$(h).removeClass("hover");$(h).animate({right:c},"fast");$(a).css("right",-c).show().animate({right:0},"fast",function(){d(c);$(h).removeClass("hidden")});j=false}else{c=$(document).width()-$(h).position().left-$(h).outerWidth();$(e).css("right",$(h).innerWidth()+1);if(document.recalc){document.recalc()}$(h).removeClass("hover");$(a).animate({right:-c},"fast");$(h).animate({right:-1},"fast",function(){$(this).addClass("hidden")});j=true}g=false};var b=function(k){var l=$(e).width()-(j?c:0);if(l<k){if(!j){i();g=true}}else{if(g){i();g=false}}};$(h).hover(function(){$(this).addClass("hover")},function(){$(this).removeClass("hover")}).bind("dragstart",function(){$("#DD-helper").show()}).bind("dragend",function(){$("#DD-helper").hide()}).bind("drag",function(k,l){x=l.offsetX;w=$(window).width();x=Math.min(w-MIN_PANEL_WIDTH,x);x=Math.max(w-MAX_PANEL_WIDTH,x);if(j){$(a).css("right",0);$(h).removeClass("hidden");j=false}d(w-x-$(this).outerWidth())}).bind("dragclickonly",function(){i()}).find("div").show();var f=function(k){if((j&&k=="show")||(!j&&k=="hide")){i()}};return{handle_minwidth_hint:b,force_panel:f}}function hide_modal(){$(".dialog-box-container").hide(0,function(){$("#overlay").hide();$("#overlay").removeClass("modal");$(".dialog-box").find(".body").children().remove()})}function show_modal(){$("#overlay").addClass("modal");_show_modal.apply(this,arguments)}function show_message(){_show_modal.apply(this,arguments)}function _show_modal(h,c,f,d,g){if(h){$(".dialog-box").find(".title").html(h);$(".dialog-box").find(".unified-panel-header").show()}else{$(".dialog-box").find(".unified-panel-header").hide()}var a=$(".dialog-box").find(".buttons").html("");if(f){$.each(f,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}var a=$(".dialog-box").find(".extra_buttons").html("");if(d){$.each(d,function(b,i){a.append($("<button/>").text(b).click(i));a.append(" ")});a.show()}else{a.hide()}if(c=="progress"){c=$("<img/>").attr("src",image_path+"/yui/rel_interstitial_loading.gif")}var e=$(".dialog-box").find(".body");e.css("min-width","");$(".dialog-box").find(".body").html(c);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").show()}e.css("min-width",e.width());if(g){g()}}function show_in_overlay(c){var d=c.width||"600";var b=c.height||"400";var a=c.scroll||"auto";$("#overlay-background").bind("click.overlay",function(){hide_modal();$("#overlay-background").unbind("click.overlay")});show_modal(null,$("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+c.url+"' width='"+d+"' height='"+b+"' scrolling='"+a+"' frameborder='0'></iframe></div>"));$("#close_button").bind("click",function(){hide_modal()})}$(function(){$(".tab").each(function(){var a=$(this).children(".submenu");if(a.length>0){if($.browser.msie){a.prepend("<iframe style=\"position: absolute; top: 0; left: 0; width: 100%; height: 100%; z-index: -1; filter:Alpha(Opacity='0');\"></iframe>")}$(this).hover(function(){a.show()},function(){a.hide()});a.click(function(){a.hide()})}})});function user_changed(a,b){if(a){$(".loggedin-only").show();$(".loggedout-only").hide();$("#user-email").text(a);if(b){$(".admin-only").show()}}else{$(".loggedin-only").hide();$(".loggedout-only").show();$(".admin-only").hide()}}; \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var P=this.data,C=this.view_start,L=this.view_end;J.save();J.fillStyle=this.prefs.block_color;J.textAlign="right";var G=this.view_end-this.view_start,D=H/G,K=this.get_row_height(),O=new m(K),A;for(var M=0,N=P.length;M<N;M++){var z=P[M],B=z[0],I=z[1],x=z[2],y=(E&&E[B]!==undefined?E[B]:null);if((I<L&&x>C)&&(this.mode=="Dense"||y!==null)){A=this.draw_element(J,this.mode,z,y,C,L,D,K,H);O.map_feature_data(z,y,A[0],A[1])}}J.restore();return O},draw_element:function(D,z,F,B,A,C,E,y,x){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,v=10,f=1,r=3,e=3,a=9,j=2,g="#ccc";var q=function(z,C,x,y,B,D,A){n.call(this,z,C,x,y,B,D,A)};t(q.prototype,n.prototype,{get_row_height:function(){var y=this.mode,x;if(y==="Dense"){x=c}else{if(y==="no_detail"){x=h}else{if(y==="Squish"){x=k}else{x=v}}}return x},draw_element:function(L,C,U,G,N,af,aj,al,x){var R=U[0],ah=U[1],Z=U[2],P=U[3],aa=Math.floor(Math.max(0,(ah-N)*aj)),M=Math.ceil(Math.min(x,Math.max(0,(Z-N)*aj))),Y=aa,ak=M,X=(C==="Dense"?0:(0+G))*al,K,ad,Q=null,an=null,A=this.prefs.block_color,ac=this.prefs.label_color;L.globalAlpha=this.alpha_scaler.gen_val(U);if(C==="Dense"){G=1}if(C==="no_detail"){L.fillStyle=A;L.fillRect(aa,X+5,M-aa,f)}else{var J=U[4],W=U[5],ab=U[6],B=U[7];if(W&&ab){Q=Math.floor(Math.max(0,(W-N)*aj));an=Math.ceil(Math.min(x,Math.max(0,(ab-N)*aj)))}var ai,S;if(C==="Squish"||C==="Dense"){ai=1;S=e}else{ai=5;S=a}if(!B){if(U.strand){if(U.strand==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(U.strand==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}}else{L.fillStyle=A}L.fillRect(aa,X,M-aa,S)}else{var I,T;if(C==="Squish"||C==="Dense"){L.fillStyle=g;I=X+Math.floor(e/2)+1;T=1}else{if(J){var I=X;var T=S;if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand")}}}else{L.fillStyle=g;I+=(e/2)+1;T=1}}L.fillRect(aa,I,M-aa,T);var D;for(var ag=0,z=B.length;ag<z;ag++){var E=B[ag],y=Math.floor(Math.max(0,(E[0]-N)*aj)),V=Math.ceil(Math.min(x,Math.max((E[1]-N)*aj)));if(y>V){continue}L.fillStyle=A;L.fillRect(y,X+(S-ai)/2+1,V-y,ai);if(Q!==undefined&&ab>W&&!(y>an||V<Q)){var ae=Math.max(y,Q),H=Math.min(V,an);L.fillRect(ae,X+1,H-ae,S);if(B.length==1&&C=="Pack"){if(J==="+"){L.fillStyle=L.canvas.manager.get_pattern("right_strand_inv")}else{if(J==="-"){L.fillStyle=L.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<H){ae+=2;H-=2}L.fillRect(ae,X+1,H-ae,S)}}}if(C==="Pack"){L.globalAlpha=1;L.fillStyle="white";var F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=g;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&this.ref_seq){var K=this.ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=g;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,X){var p=f("class").extend,s=f("slotting"),M=f("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",t="Currently indexing... please wait",x="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",d=10,u=5,B=5;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,am,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get_data_from_cache(af,aj,ak);if(ah){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ak,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get_data_from_cache(an,ai,am);if(!ao){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.container_div=$("<div/>").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_icons()};p(Q.prototype,q.prototype,y.prototype,{update_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))-ai.width()/2,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;this.content_visible=true;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.toggle_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Hide/show track content").addClass("icon-button toggle").tipsy({gravity:"s"}).appendTo(this.icons_div);this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.toggle_icon.click(function(){if(ak.content_visible){ak.toggle_icon.addClass("toggle-expand").removeClass("toggle");ak.hide_contents();ak.mode_div.hide();ak.content_visible=false}else{ak.toggle_icon.addClass("toggle").removeClass("toggle-expand");ak.content_visible=true;ak.mode_div.show();ak.show_contents()}});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!this.content_visible){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.set_painter_from_config()};p(e.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an,az));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(af,ak,ag,aj,an,am,ah){e.call(this,af,ak,ag,aj,an,am,ah);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2],Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/scripts/packed/trackster_ui.js --- a/static/scripts/packed/trackster_ui.js +++ b/static/scripts/packed/trackster_ui.js @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}view.update_intro_div();var n;for(var j=0;j<view.drawables.length;j++){if(view.drawables[j].name===m){view.set_overview(view.drawables[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})}; \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -650,8 +650,13 @@ */ /** - * Base interface for all drawable objects. Drawable objects have a name and are - * associated with a view and container. They optionally have a drag handle class. + * Base class for all drawable objects. Drawable objects are associated with a view and live in a + * container. They have the following HTML elements and structure: + * <container_div> + * <header_div> + * <content_div> + * + * They optionally have a drag handle class. */ var Drawable = function(name, view, container, prefs, drag_handle_class) { if (!Drawable.id_counter) { Drawable.id_counter = 0; } @@ -672,6 +677,33 @@ this.prefs = this.config.values; this.drag_handle_class = drag_handle_class; this.is_overview = false; + + // FIXME: this should be a saved setting + this.content_visible = true; + + // Build Drawable HTML and behaviors. + this.container_div = this.build_container_div(); + this.header_div = this.build_header_div(); + + if (this.header_div) { + this.container_div.append(this.header_div); + + this.icons_div = this.build_icons_div().hide(); + this.header_div.append(this.icons_div); + + // Suppress double clicks in header so that they do not impact viz. + this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Show icons when users is hovering over track. + var drawable = this; + this.container_div.hover( + function() { drawable.icons_div.show(); }, + function() { drawable.icons_div.hide(); } + ); + + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); + } }; extend(Drawable.prototype, { @@ -701,13 +733,37 @@ remove: function() { this.container.remove_drawable(this); - this.container_div.fadeOut('slow', function() { + this.container_div.hide(0, function() { $(this).remove(); // HACK: is there a better way to update the view? view.update_intro_div(); view.has_changes = true; }); - } + }, + /** + * Build drawable's container div; this is the parent div for all drawable's elements. + */ + build_container_div: function() {}, + /** + * Build drawable's header div. + */ + build_header_div: function() {}, + /** + * Build drawable's icons div. + */ + build_icons_div: function() {}, + /** + * Update icons. + */ + update_icons: function() {}, + /** + * Hide drawable's contents. + */ + hide_contents: function () {}, + /** + * Show drawable's contents. + */ + show_contents: function() {} }); /** @@ -805,36 +861,54 @@ var DrawableGroup = function(name, view, container, prefs) { DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); - // HTML elements. - this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); - this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); - this.header_div.append($("<div/>").addClass(this.drag_handle_class)); - this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); - this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); - // Set up containers/moving for group: register both container_div and content div as container // because both are used as containers (container div to recognize container, content_div to // store elements). Group can be moved. + this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); is_container(this.container_div, this); is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - - this.update_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { - /** - * Make popup menu for group. - */ - update_icons: function() { + build_container_div: function() { + return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); + }, + build_header_div: function() { + var header_div = $("<div/>").addClass("track-header"); + header_div.append($("<div/>").addClass(this.drag_handle_class)); + this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div); + return header_div; + }, + build_icons_div: function() { + var icons_div = $("<div/>").css("float", "left"); + + this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show group content") + .addClass("icon-button toggle").tipsy( {gravity: 's'} ) + .appendTo(icons_div); + this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") + .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) + .appendTo(icons_div); + this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") + .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) + .appendTo(icons_div); var group = this; - - var group_dropdown = {}; - - // - // Edit config option. - // - group_dropdown["Edit configuration"] = function() { + + // Toggle icon hides or shows the group content. + this.toggle_icon.click( function() { + if ( group.content_visible ) { + group.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + group.hide_contents(); + group.content_visible = false; + } else { + group.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + group.content_visible = true; + group.show_contents(); + } + }); + + // Clicking on settings icon opens group config. + this.settings_icon.click( function() { var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { group.config.update_from_form( $(".dialog-box") ); @@ -854,16 +928,25 @@ "Cancel": cancel_fn, "OK": ok_fn }); - }; + }); - // - // Remove option. - // - group_dropdown.Remove = function() { + // Clicking on remove icon removes group. + this.remove_icon.click( function() { + // Tipsy for remove icon must be deleted when group is deleted. + $(".tipsy").remove(); group.remove(); - }; + }); - make_popupmenu(group.name_div, group_dropdown); + return icons_div; + }, + hide_contents : function () { + this.content_div.hide(); + }, + show_contents : function() { + // Show the contents div and labels (if present) + this.content_div.show(); + // Request a redraw of the content + this.request_draw(); } }); @@ -909,7 +992,7 @@ this.content_div = this.viewport_container; is_container(this.viewport_container, view); // Introduction div shown when there are no tracks. - this.intro_div = $("<div/>").addClass("intro"); + this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { add_tracks(); }); @@ -1027,6 +1110,7 @@ // Only act on x axis scrolling if we see if, y will be i // handled by the browser when the event bubbles up if ( dx ) { + dx *= 50; var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) ); view.move_delta( delta_chrom ); } @@ -1076,10 +1160,10 @@ /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.drawables.length === 0) { - this.intro_div.appendTo(this.viewport_container); + this.intro_div.show(); } else { - this.intro_div.remove(); + this.intro_div.hide(); } }, update_location: function(low, high) { @@ -1255,7 +1339,7 @@ DrawableCollection.prototype.remove_drawable.call(this, drawable); if (hide) { var view = this; - drawable.container_div.fadeOut('slow', function() { + drawable.container_div.hide(0, function() { $(this).remove(); view.update_intro_div(); }); @@ -2114,31 +2198,49 @@ build_form: function() { var track_config = this; var container = $("<div />"); - $.each( this.params, function( index, param ) { - if ( ! param.hidden ) { + var param; + // Function to process parameters recursively + function handle_params( params, container ) { + for ( var index = 0; index < params.length; index++ ) { + param = params[index]; + // Hidden params have no representation in the form + if ( param.hidden ) { continue; } + // Build row for param var id = 'param_' + index; var value = track_config.values[ param.key ]; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); + // Draw parameter as checkbox if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); + // Draw parameter as textbox } else if ( param.type === 'text' ) { row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select() })); + // Draw paramter as select area + } else if ( param.type == 'select' ) { + var select = $('<select />').attr("id", id); + for ( var i = 0; i < param.options.length; i++ ) { + $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); + } + select.val( value ); + row.append( select ); + // Draw parameter as color picker } else if ( param.type === 'color' ) { var input = $('<input />').attr("id", id ).attr("name", id ).val( value ); // Color picker in tool tip style float - var tip = $( "<div class='tipsy tipsy-north' style='position: absolute;' />" ).hide(); + var tip = $( "<div class='tipsy tipsy-west' style='position: absolute;' />" ).hide(); // Inner div for padding purposes var tip_inner = $("<div style='background-color: black; padding: 10px;'></div>").appendTo(tip); var farb_container = $("<div/>") .appendTo(tip_inner) .farbtastic( { width: 100, height: 100, callback: input, color: value }); - // Outer div container input and tip for hover to work $("<div />").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) { tip.css( { - left: $(this).position().left + ( $(input).width() / 2 ) - 60, - top: $(this).position().top + $(this.height) + // left: $(this).position().left + ( $(input).width() / 2 ) - 60, + // top: $(this).position().top + $(this.height) + left: $(this).position().left + $(input).width() + 5, + top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(input).height() / 2 ) } ).show(); $(document).bind( "click.color-picker", function() { tip.hide(); @@ -2150,8 +2252,15 @@ else { row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); } + // Help text + if ( param.help ) { + row.append( $("<div class='help'/>").text( param.help ) ); + } } - }); + } + // Handle top level parameters in order + handle_params( this.params, container ); + // Return element containing constructed form return container; }, update_from_form: function( container ) { @@ -2229,7 +2338,16 @@ // Only show popups in Pack mode. if (tile.mode !== "Pack") { return; } - $(this.canvas).mousemove(function (e) { + $(this.canvas).hover( function() { + this.hovered = true; + $(this).mousemove(); + }, function() { + this.hovered = false; + // Clear popup if it is still hanging around (this is probably not needed) + $(this).siblings(".feature-popup").remove(); + } ).mousemove(function (e) { + // Use the hover plugin to get a delay before showing popup + if ( !this.hovered ) { return; } // Get feature data for position. var this_offset = $(this).offset(), @@ -2270,8 +2388,8 @@ // Build popup. var popup = $("<div/>").attr("id", feature_uid).addClass("feature-popup"), - key, value, - table = $("<table/>").appendTo(popup), row; + table = $("<table/>"), + key, value, row; for (key in feature_dict) { value = feature_dict[key]; row = $("<tr/>").appendTo(table); @@ -2279,6 +2397,7 @@ $("<td/>").attr("align", "left").appendTo(row) .text(typeof(value) == 'number' ? round(value, 2) : value); } + popup.append( $("<div class='feature-popup-inner'>").append( table ) ); popups[feature_uid] = popup; } @@ -2289,7 +2408,7 @@ // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not // overlap popup. var - popupX = offsetX + parseInt( tile.canvas.css("left") ) + 7, + popupX = offsetX + parseInt( tile.canvas.css("left") ) - popup.width() / 2, popupY = offsetY + parseInt( tile.canvas.css("top") ) + 7; popup.css("left", popupX + "px").css("top", popupY + "px") } @@ -2320,7 +2439,7 @@ * -------> ReadTrack * -------> VcfTrack */ -var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, prefs, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2331,41 +2450,89 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - + + if (!Track.id_counter) { Track.id_counter = 0; } + this.id = Track.id_counter++; + // - // Create HTML element structure for track. + // Create content div, which is where track is displayed. // - this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); - - // Create and initialize track header and icons. - if (show_header) { - this.header_div = $("<div class='track-header' />").appendTo(this.container_div); - if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } - this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) + this.content_div = $("<div class='track-content'>").appendTo(this.container_div); + this.container.content_div.append(this.container_div); +}; +extend(Track.prototype, Drawable.prototype, { + build_container_div: function () { + return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + }, + build_header_div: function() { + var header_div = $("<div class='track-header'/>"); + if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); } + this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.name) .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); - this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); - + return header_div; + }, + build_icons_div: function() { + var icons_div = $("<div/>").css("float", "left"); + // Track icons. + this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") + .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(icons_div); + this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") + .addClass("icon-button toggle").tipsy( {gravity: 's'} ) + .appendTo(icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview") .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div).hide(); + .appendTo(icons_div).hide(); this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools") .addClass("icon-button tools-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div).hide(); + .appendTo(icons_div).hide(); this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); var track = this; - - // Suppress double clicks in header so that they do not impact viz. - this.header_div.dblclick( function(e) { e.stopPropagation(); } ); - + + // Set up behavior for modes popup. + if (track.display_modes !== undefined) { + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); + track.mode = init_mode; + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); + + var mode_mapping = {}; + for (var i = 0, len = track.display_modes.length; i < len; i++) { + var mode = track.display_modes[i]; + mode_mapping[mode] = function(mode) { + return function() { + track.change_mode(mode); + // HACK: the popup menu messes with the track's hover event, so manually show/hide + // icons div for now. + track.icons_div.show(); + track.container_div.mouseleave(function() { track.icons_div.hide(); } ); }; + }(mode); + } + + make_popupmenu(this.mode_icon, mode_mapping); + } + + // Toggle icon hides or shows the track content. + this.toggle_icon.click( function() { + if ( track.content_visible ) { + track.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + track.hide_contents(); + track.content_visible = false; + } else { + track.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + track.content_visible = true; + track.show_contents(); + } + }); + // Clicking on settings icon opens track config. this.settings_icon.click( function() { var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, @@ -2388,22 +2555,22 @@ "OK": ok_fn }); }); - + this.overview_icon.click( function() { track.view.set_overview(track); }); - + this.filters_icon.click( function() { // TODO: update tipsy text. track.filters_div.toggle(); track.filters_manager.reset_filters(); }); - + this.tools_icon.click( function() { // TODO: update tipsy text. - + track.dynamic_tool_div.toggle(); - + // Update track name. if (track.dynamic_tool_div.is(":visible")) { track.set_name(track.name + track.tool_region_and_parameters_str()); @@ -2414,7 +2581,7 @@ // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. $(".tipsy").remove(); }); - + // Clicking on remove icon removes track. this.remove_icon.click( function() { // Tipsy for remove icon must be deleted when track is deleted. @@ -2422,44 +2589,31 @@ track.remove(); }); - // Set up behavior for modes popup. - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); - } - - this.header_div.append( $("<div/>").css("clear", "both") ); - - // Set up config icon. - - // Show icons when users is hovering over track. - this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - } - } - - // - // Create content div, which is where track is displayed. - // - this.content_div = $("<div class='track-content'>").appendTo(this.container_div); - this.container.content_div.append(this.container_div); -}; -extend(Track.prototype, Drawable.prototype, { - /** Returns track type. */ + return icons_div; + }, + /** + * Hide any elements that are part of the tracks contents area. Should + * remove as approprite, the track will be redrawn by show_contents. + */ + hide_contents : function () { + // Clear contents by removing any elements that are contained in + // the tracks content_div + this.content_div.children().remove(); + // Hide the content div + this.content_div.hide(); + // And any y axis labels (common to several track types) + this.container_div.find(".yaxislabel, .track-resize").hide() + }, + show_contents : function() { + // Show the contents div and labels (if present) + this.content_div.show(); + this.container_div.find(".yaxislabel, .track-resize").show() + // Request a redraw of the content + this.request_draw(); + }, + /** + * Returns track type. + */ get_type: function() { // Order is important: start with most-specific classes and go up the track hierarchy. if (this instanceof LabelTrack) { @@ -2557,8 +2711,8 @@ predraw_init: function() {} }); -var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) { - Track.call(this, name, view, container, show_header, prefs); +var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict) { + Track.call(this, name, view, container, prefs); var track = this, view = track.view; @@ -2616,12 +2770,12 @@ */ change_mode: function(name) { var track = this; - track.mode_div.text(name); // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = name; track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); + this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); return track; }, /** @@ -2682,6 +2836,11 @@ */ _draw: function(force, clear_after) { if (!this.enabled) { return; } + + // TODO: There should probably be a general way to disable content drawing + // for all drawables. However the button to toggle this is currently + // only present for Track instances. + if (!this.content_visible) { return; } // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot. if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; } @@ -2694,7 +2853,7 @@ w_scale = width / range, resolution = this.view.resolution, parent_element = $("<div style='position: relative;'></div>"); - + // For overview, adjust high, low, resolution, and w_scale. if (this.is_overview) { low = this.view.max_low; @@ -2946,6 +3105,7 @@ this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -2972,7 +3132,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); view.reference_track = this; this.left_offset = 200; @@ -2987,6 +3147,7 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -3024,11 +3185,12 @@ var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - TiledTrack.call( this, name, view, container, true, prefs ); + TiledTrack.call( this, name, view, container, prefs ); this.min_height_px = 16; this.max_height_px = 400; - this.height_px = 80; + // Default height for new tracks, should be a defined constant? + this.height_px = 32; this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; @@ -3076,8 +3238,10 @@ var drag_control = $( "<div class='track-resize'>" ) // Control shows on hover over track, stays while dragging $(track.container_div).hover( function() { - in_handle = true; - drag_control.show(); + if ( track.content_visible ) { + in_handle = true; + drag_control.show(); + } }, function() { in_handle = false; if ( ! in_drag ) { drag_control.hide(); } @@ -3108,9 +3272,20 @@ track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { - track.prefs.min_value = data.min; - track.prefs.max_value = data.max; + // Compute default minimum and maximum values + var min_value = data.min + var max_value = data.max + // If mean and sd are present, use them to compute a ~95% window + // but only if it would shrink the range on one side + min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) ) + max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) ) + // Update the prefs + track.prefs.min_value = min_value; + track.prefs.max_value = max_value; // Update the config + // FIXME: we should probably only save this when the user explicately sets it + // since we lose the ability to compute it on the fly (when changing + // chromosomes for example). $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value); $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value); } @@ -3170,7 +3345,7 @@ // // Initialization. // - TiledTrack.call(this, name, view, container, true, prefs, filters, tool); + TiledTrack.call(this, name, view, container, prefs, filters, tool); // Define and restore track configuration. this.config = new DrawableConfig( { @@ -3179,13 +3354,17 @@ { key: 'name', label: 'Name', type: 'text', default_value: name }, { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() }, { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' }, - { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, + { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true, + help: 'Show the number of items in each bin when drawing summary histogram' }, + { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones', + options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, ], saved_values: prefs, onchange: function() { track.set_name(track.prefs.name); track.tile_cache.clear(); + track.set_painter_from_config(); track.request_draw(); } }); @@ -3205,9 +3384,17 @@ this.data_manager = new DataManager(20, this); this.left_offset = 200; - this.painter = painters.LinkedFeaturePainter; + // this.painter = painters.LinkedFeaturePainter; + this.set_painter_from_config(); }; extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + set_painter_from_config: function() { + if ( this.config.values['connector_style'] == 'arcs' ) { + this.painter = painters.ArcLinkedFeaturePainter; + } else { + this.painter = painters.LinkedFeaturePainter; + } + }, /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. @@ -3294,13 +3481,14 @@ } }, update_auto_mode: function( mode ) { + var mode; if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { mode = "feature spans"; } else if ( mode == "summary_tree" ) { mode = "coverage histogram"; } - this.mode_div.text( "Auto (" + mode + ")" ); + this.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")"); } }, /** @@ -3527,7 +3715,7 @@ var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null); // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq); - var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required)); + var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required,width)); var canvas = this.view.canvas_manager.new_canvas(); var feature_mapper = null; @@ -4057,6 +4245,7 @@ this.feature_positions = {}; this.slot_height = slot_height; this.translation = 0; + this.y_translation = 0; }; /** @@ -4078,7 +4267,7 @@ */ FeaturePositionMapper.prototype.get_feature_data = function(x, y) { // Find slot using Y. - var slot = Math.floor( y/this.slot_height ), + var slot = Math.floor( (y-this.y_translation)/this.slot_height ), feature_dict; // May not be over a slot due to padding, margin, etc. @@ -4108,15 +4297,23 @@ FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" }; extend(FeaturePainter.prototype, { - get_required_height: function(rows_required) { + get_required_height: function(rows_required, width) { // y_scale is the height per row var required_height = y_scale = this.get_row_height(), mode = this.mode; // If using a packing mode, need to multiply by the number of slots used if (mode === "no_detail" || mode === "Squish" || mode === "Pack") { required_height = rows_required * y_scale; } + return required_height + this.get_top_padding(width) + this.get_bottom_padding(width); + }, + /** Extra padding before first row of features */ + get_top_padding: function(width) { + return 0; + }, + /** Extra padding after last row of features */ + get_bottom_padding: function(width) { // Pad bottom by half a row, at least 5 px - return required_height + Math.max( Math.round( y_scale / 2 ), 5 ); + return Math.max( Math.round( this.get_row_height() / 2 ), 5 ) }, /** * Draw data on ctx using slots and within the rectangle defined by width and height. Returns @@ -4153,6 +4350,7 @@ } ctx.restore(); + feature_mapper.y_translation = this.get_top_padding(width); return feature_mapper; }, /** @@ -4171,7 +4369,7 @@ SQUISH_TRACK_HEIGHT = 5, PACK_TRACK_HEIGHT = 10, NO_DETAIL_FEATURE_HEIGHT = 1, - DENSE_FEATURE_HEIGHT = 3, + DENSE_FEATURE_HEIGHT = 9, SQUISH_FEATURE_HEIGHT = 3, PACK_FEATURE_HEIGHT = 9, LABEL_SPACING = 2, @@ -4179,6 +4377,10 @@ var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) { FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler); + // Whether to draw a single connector in the background that spans the entire feature (the intron fishbone) + this.draw_background_connector = true; + // Whether to call draw_connector for every pair of blocks + this.draw_individual_connectors = false; }; extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, { @@ -4216,7 +4418,7 @@ f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), draw_start = f_start, draw_end = f_end, - y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, + y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width), thickness, y_start, thick_start = null, thick_end = null, // TODO: is there any reason why block, label color cannot be set at the Painter level? block_color = this.prefs.block_color, @@ -4240,7 +4442,9 @@ var feature_strand = feature[4], feature_ts = feature[5], feature_te = feature[6], - feature_blocks = feature[7]; + feature_blocks = feature[7], + // Whether we are drawing full height or squished features + full_height = true; if (feature_ts && feature_te) { thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) ); @@ -4249,9 +4453,13 @@ // Set vars that depend on mode. var thin_height, thick_height; - if (mode === "Squish" || mode === "Dense" ) { + if (mode === "Squish" ) { thin_height = 1; thick_height = SQUISH_FEATURE_HEIGHT; + full_height = false; + } else if ( mode === "Dense" ) { + thin_height = 5; + thick_height = DENSE_FEATURE_HEIGHT; } else { // mode === "Pack" thin_height = 5; thick_height = PACK_FEATURE_HEIGHT; @@ -4260,17 +4468,17 @@ // Draw feature/feature blocks + connectors. if (!feature_blocks) { // If there are no blocks, treat the feature as one big exon. - if ( feature.strand ) { - if (feature.strand === "+") { + ctx.fillStyle = block_color; + ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height); + // If strand is specified, draw arrows over feature + if ( feature_strand && full_height ) { + if (feature_strand === "+") { ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' ); - } else if (feature.strand === "-") { + } else if (feature_strand === "-") { ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' ); } + ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height); } - else { // No strand. - ctx.fillStyle = block_color; - } - ctx.fillRect(f_start, y_center, f_end - f_start, thick_height); } else { // // There are feature blocks and mode is either Squish or Pack. @@ -4279,38 +4487,51 @@ // needed. This ensures that whole feature, regardless of whether it starts with // a block, is visible. // - - // Draw whole feature as connector/intron. + + // Compute y axis center position and height var cur_y_center, cur_height; if (mode === "Squish" || mode === "Dense") { - ctx.fillStyle = CONNECTOR_COLOR; cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } else { // mode === "Pack" if (feature_strand) { - var cur_y_center = y_center; - var cur_height = thick_height; - if (feature_strand === "+") { - ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' ); - } else if (feature_strand === "-") { - ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' ); - } + cur_y_center = y_center; + cur_height = thick_height; } else { - ctx.fillStyle = CONNECTOR_COLOR; cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } } - ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height); + + // Draw whole feature as connector/intron. + if ( this.draw_background_connector ) { + if (mode === "Squish" || mode === "Dense") { + ctx.fillStyle = CONNECTOR_COLOR; + } + else { // mode === "Pack" + if (feature_strand) { + if (feature_strand === "+") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' ); + } else if (feature_strand === "-") { + ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' ); + } + } + else { + ctx.fillStyle = CONNECTOR_COLOR; + } + } + ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height); + } // Draw blocks. var start_and_height; for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); + block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ), + last_block_start, last_block_end; // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -4341,6 +4562,12 @@ ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height ); } } + // Draw individual connectors if required + if ( this.draw_individual_connectors && last_block_start ) { + this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_center ); + } + last_block_start = block_start; + last_block_end = block_end; } // FIXME: Height scaling only works in Pack mode right now. @@ -4673,11 +4900,54 @@ } }); +var ArcLinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) { + LinkedFeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler); + // Need to know the longest feature length for adding spacing + this.longest_feature_length = this.calculate_longest_feature_length(); + this.draw_background_connector = false; + this.draw_individual_connectors = true; +}; + +extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, { + + calculate_longest_feature_length: function () { + var longest_feature_length = 0; + for (var i = 0, len = this.data.length; i < len; i++) { + var feature = this.data[i], feature_start = feature[1], feature_end = feature[2]; + longest_feature_length = Math.max( longest_feature_length, feature_end - feature_start ); + } + return longest_feature_length; + }, + + get_top_padding: function( width ) { + var view_range = this.view_end - this.view_start, + w_scale = width / view_range; + return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) ); + }, + + draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_center ) { + // Arc drawing -- from closest endpoints + var x_center = ( block1_end + block2_start ) / 2, + radius = block2_start - x_center; + // For full half circles + var angle1 = Math.PI, angle2 = 0; + if ( radius > 0 ) { + ctx.beginPath(); + ctx.arc( x_center, y_center, block2_start - x_center, Math.PI, 0 ); + ctx.stroke(); + } + } +}); + + + + exports.Scaler = Scaler; exports.SummaryTreePainter = SummaryTreePainter; exports.LinePainter = LinePainter; exports.LinkedFeaturePainter = LinkedFeaturePainter; exports.ReadPainter = ReadPainter; +exports.ArcLinkedFeaturePainter = ArcLinkedFeaturePainter; // End painters_module encapsulation }; @@ -4708,4 +4978,4 @@ for ( key in modules.trackster ) { target[key] = modules.trackster[key]; } -})(window); \ No newline at end of file +})(window); diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/admin/select_tool_panel_section.mako --- a/templates/admin/select_tool_panel_section.mako +++ b/templates/admin/select_tool_panel_section.mako @@ -23,7 +23,7 @@ <br/><div class="toolForm"> - <div class="toolFormTitle">Load tools into tool panel</div> + <div class="toolFormTitle">Choose section to load tools into tool panel</div><div class="toolFormBody"><form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" > %if shed_tool_conf_select_field: @@ -40,10 +40,17 @@ <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/> %endif <div class="form-row"> - <label>Tool panel section:</label> + <label>Add new tool panel section:</label> + <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + Add a new tool panel section or choose an existing section in your tool panel below to contain the installed tools. + </div> + </div> + <div class="form-row"> + <label>Select existing tool panel section:</label> ${tool_panel_section_select_field.get_html()} <div class="toolParamHelp" style="clear: both;"> - Choose the section in your tool panel to contain the installed tools. + Choose an existing section in your tool panel to contain the installed tools. </div></div><div class="form-row"> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -103,7 +103,7 @@ <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> ${workflow_name} <div popupmenu="workflow-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a></div></div></td> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/embed_base.mako --- a/templates/embed_base.mako +++ b/templates/embed_base.mako @@ -44,7 +44,7 @@ <div style="float: left"><a class="display_in_embed icon-button toggle-expand tooltip" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}" title="Show ${item_display_name} content"></a> - <a class="toggle-contract icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a> + <a class="toggle icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a></div><div style="float: right;"> ${self.render_item_links( item )} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/library/common/import_datasets_to_histories.mako --- a/templates/library/common/import_datasets_to_histories.mako +++ b/templates/library/common/import_datasets_to_histories.mako @@ -49,12 +49,12 @@ <div class="toolFormTitle">Destination Histories:</div><div class="toolFormBody"><div class="form-row" id="single-destination"> - <select id="single-dest-select" name="target_history_ids"> + <select id="single-dest-select" name="target_history_id"> %for i, target_history in enumerate( target_histories ): <% encoded_id = trans.security.encode_id( target_history.id ) - if encoded_id == selected_history_id: - selected_text = " selected" + if encoded_id == target_history_id: + selected_text = " selected='selected'" else: selected_text = "" if target_history == current_history: diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/page/display.mako --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -26,7 +26,7 @@ container.find(".summary-content").hide("fast"); container.find(".item-content").html(item_content).show("fast"); container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); + container.find(".toggle").show(); // Init needed for history items. init_history_items( container.find("div.historyItemWrapper"), "noinit", "nochanges" ); @@ -43,7 +43,7 @@ container.find(".summary-content").hide("fast"); container.find(".item-content").show("fast"); container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); + container.find(".toggle").show(); } }; @@ -51,7 +51,7 @@ var hide_embedded_item = function() { container.find(".item-content").hide("fast"); container.find(".summary-content").show("fast"); - container.find(".toggle-contract").hide(); + container.find(".toggle").hide(); container.find(".toggle-expand").show(); }; @@ -63,7 +63,7 @@ }); // Setup toggle contract. - var toggle_contract = $(this).find('.toggle-contract'); + var toggle_contract = $(this).find('.toggle'); toggle_contract.click( function() { hide_embedded_item(); return false; @@ -89,7 +89,7 @@ ${parent.stylesheets()} ${h.css( "base", "history", "autocomplete_tagging" )} <style type="text/css"> - .toggle-contract { display: none; } + .toggle { display: none; } .embedded-item h4 { margin: 0px; } diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -432,7 +432,7 @@ <div id="top-links" class="historyLinks"><a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a> - <a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none;"></a> + <a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none"></a> %if trans.get_user(): <div style="width: 40px; float: right; white-space: nowrap;"> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,7 +42,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy" )} <script type="text/javascript"> // @@ -110,6 +110,52 @@ } }); }; + + /** + * Use a popup grid to bookmarks from a dataset. + */ + var add_bookmarks = function() { + show_modal( "Select dataset for new bookmarks", "progress" ); + $.ajax({ + url: "${h.url_for( action='list_histories' )}", + data: { "f-dbkey": view.dbkey }, + error: function() { alert( "Grid failed" ); }, + success: function(table_html) { + show_modal( + "Select dataset for new bookmarks", + table_html, { + "Cancel": function() { + hide_modal(); + }, + "Insert": function() { + // Just use the first selected + $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){ + var data, id = $(this).val(); + if ($(this).attr("name") === "id") { + data = { hda_id: id }; + } else { + data = { ldda_id: id}; + } + + $.ajax({ + url: "${h.url_for( action='bookmarks_from_dataset' )}", + data: data, + dataType: "json", + }).then( function(data) { + for( i = 0; i < data.data.length; i++ ) { + var row = data.data[i]; + console.log( row[0], row[1] ); + add_bookmark( row[0], row[1] ); + } + }); + }); + hide_modal(); + } + } + ); + } + }); + }; $(function() { // Manual tipsy config because default gravity is S and cannot be changed. @@ -240,7 +286,13 @@ annotation = "Bookmark description"; return add_bookmark(position, annotation); }); - + + // make_popupmenu( $("#bookmarks-more-button"), { + // "Add from BED dataset": function() { + // add_bookmarks(); + // } + // }); + init_keyboard_nav(view); }; @@ -271,14 +323,15 @@ <div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"> + <div style="float: right"> + <a id="add-bookmark-button" class='icon-button menu-button plus-button' href="javascript:void(0);" title="Add bookmark"></a> + ## <a id="bookmarks-more-button" class='icon-button menu-button gear popup' href="javascript:void(0);" title="More actions"></a> + </div> Bookmarks </div></div><div class="unified-panel-body" style="overflow: auto;"><div id="bookmarks-container"></div> - <div> - <a class="icon-button import" style="margin-left: .5em; width: 100%" original-title="Add Bookmark" id="add-bookmark-button" href="javascript:void(0);">Add Bookmark</a> - </div></div></%def> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -97,7 +97,7 @@ %if can_browse_contents: <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name}</div> + <div class="toolFormTitle">Browse ${repository.name} revision ${repository.tip} (repository tip)</div> %if can_download: <div class="form-row"><label>Clone this repository:</label> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def> -<%def name="render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"><% from galaxy.webapps.community.controllers.common import encode, decode %> %if metadata or can_set_metadata: <p/> @@ -195,6 +195,45 @@ </div><div style="clear: both"></div> %endif + %if 'datatypes' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Data types</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% datatypes_dicts = metadata[ 'datatypes' ] %> + <table class="grid"> + <tr> + <td><b>extension</b></td> + <td><b>dtype</b></td> + <td><b>mimetype</b></td> + </tr> + %for datatypes_dict in datatypes_dicts: + <% + extension = datatypes_dict[ 'extension' ] + dtype = datatypes_dict[ 'dtype' ] + mimetype = datatypes_dict[ 'mimetype' ] + %> + <tr> + <td>${extension}</td> + <td>${dtype}</td> + <td> + %if mimetype: + ${mimetype} + %else: +   + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %endif %if can_set_metadata: <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -13,9 +13,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -16,9 +16,9 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip %> @@ -184,7 +184,7 @@ </form></div></div> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, can_set_metadata=True )} +${render_repository_items( repository_metadata_id, metadata, can_set_metadata=True )} <p/><div class="toolForm"><div class="toolFormTitle">Manage categories</div> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -13,9 +13,9 @@ can_browse_contents = not is_new can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! @@ -104,4 +104,4 @@ </div></div><p/> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -16,9 +16,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -18,9 +18,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><html> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -64,7 +64,13 @@ <div class="toolForm"><div class="toolFormTitle">Upload a single file or a tarball</div><div class="toolFormBody"> - ## TODO: nginx + <div class="form-row"> + <div class="warningmessage"> + Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your + browser after clicking the <b>Upload</b> button below. + </div> + <div style="clear: both"></div> + </div><form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"><div class="form-row"><label>File:</label> @@ -73,7 +79,16 @@ </div><div style="clear: both"></div></div> - + <div class="form-row"> + <label>Url:</label> + <div class="form-row-input"> + <input name="url" type="textfield" value="${url}" size="40"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Enter a URL to upload your files via http. + </div> + <div style="clear: both"></div> + </div><div class="form-row"><% if uncompress_file: diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -15,9 +15,9 @@ can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -16,9 +16,9 @@ can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -14,9 +14,9 @@ can_browse_contents = webapp == 'community' and not is_new can_view_change_log = webapp == 'community' and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! @@ -186,7 +186,7 @@ %endif </div></div> -${render_repository_tools_and_workflows( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} %if repository.categories: <p/><div class="toolForm"> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -17,9 +17,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = webapp == 'community' and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -20,9 +20,9 @@ can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user can_view_change_log = in_tool_shed and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -213,7 +213,7 @@ show_workflow_parameters(); }, beforeSubmit: function( data ) { - show_modal( "Loading workflow", "progress" ); + show_message( "Loading workflow", "progress" ); } }); } @@ -650,7 +650,7 @@ }; var save_current_workflow = function ( eventObj, success_callback ) { - show_modal( "Saving workflow", "progress" ); + show_message( "Saving workflow", "progress" ); workflow.check_changes_in_active_form(); if (!workflow.has_changes) { hide_modal(); diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca test-data/fastqc_report.html --- a/test-data/fastqc_report.html +++ b/test-data/fastqc_report.html @@ -1,117 +1,224 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Strict//EN"><html> -<head><title>1000gsample.fastq FastQC Report</title> +<head><title>dataset_1.dat FastQC Report</title><style type="text/css"> - body { - font-family: sans-serif; - color: #000000; - background-color: #FFFFFF; - border: 0; - margin: 0; - padding: 0; - } + @media screen { + div.summary { + width: 18em; + position:fixed; + top: 3em; + margin:1em 0 0 1em; + } + + div.main { + display:block; + position:absolute; + overflow:auto; + height:auto; + width:auto; + top:4.5em; + bottom:2.3em; + left:18em; + right:0; + border-left: 1px solid #CCC; + padding:0 0 0 1em; + background-color: white; + z-index:1; + } + + div.header { + background-color: #EEE; + border:0; + margin:0; + padding: 0.5em; + font-size: 200%; + font-weight: bold; + position:fixed; + width:100%; + top:0; + left:0; + z-index:2; + } + + div.footer { + background-color: #EEE; + border:0; + margin:0; + padding:0.5em; + height: 1.3em; + overflow:hidden; + font-size: 100%; + font-weight: bold; + position:fixed; + bottom:0; + width:100%; + z-index:2; + } + + img.indented { + margin-left: 3em; + } + } + + @media print { + img { + max-width:100% !important; + page-break-inside: avoid; + } + h2, h3 { + page-break-after: avoid; + } + div.header { + background-color: #FFF; + } + + } + + body { + font-family: sans-serif; + color: #000; + background-color: #FFF; + border: 0; + margin: 0; + padding: 0; + } + + div.header { + border:0; + margin:0; + padding: 0.5em; + font-size: 200%; + font-weight: bold; + width:100%; + } + + #header_title { + display:inline-block; + float:left; + clear:left; + } + #header_filename { + display:inline-block; + float:right; + clear:right; + font-size: 50%; + margin-right:2em; + text-align: right; + } + + div.header h3 { + font-size: 50%; + margin-bottom: 0; + } + + div.summary ul { + padding-left:0; + list-style-type:none; + } + + div.summary ul li img { + margin-bottom:-0.5em; + margin-top:0.5em; + } + + div.main { + background-color: white; + } - div.header { - background-color: #EEEEEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 200%; - font-weight: bold; - } + div.module { + padding-bottom:1.5em; + padding-top:1.5em; + } + + div.footer { + background-color: #EEE; + border:0; + margin:0; + padding: 0.5em; + font-size: 100%; + font-weight: bold; + width:100%; + } - div.footer { - background-color: #EEEEEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 100%; - font-weight: bold; - } - div.main { - margin-left: 2em; - margin-right: 2em; - } + a { + color: #000080; + } + + a:hover { + color: #800000; + } - div.module { - padding-bottom:1.5em; - padding-top:1.5em; - } + h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear:left; + } - a { - color: #000080; - } + table { + margin-left: 3em; + text-align: center; + } + + th { + text-align: center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } + + td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } - a:hover { - color: #800000; - } - - h2 { - color: #800000; - padding-bottom: 0; - margin-bottom: 0; - } + img { + padding-top: 0; + margin-top: 0; + border-top: 0; + } - table { - margin-left: 3em; - text-align: center; - } - - th { - text-align: center; - background-color: #000080; - color: #FFFFFF; - padding: 0.4em; - } - - td { - font-family: monospace; - text-align: left; - background-color: #EEEEEE; - color: #000000; - padding: 0.4em; - } - - img { - padding-top: 0; - margin-top: 0; - border-top: 0; - } - - img.indented { - margin-left: 3em; - } - - p { - padding-top: 0; - margin-top: 0; - } + + p { + padding-top: 0; + margin-top: 0; + } + </style></head><body> -<div class="header"><img src="Icons/fastqc_icon.png">FastQC Report</div> +<div class="header"> +<div id="header_title"><img src="fastqc_icon.png" alt="FastQC">FastQC Report</div> +<div id="header_filename"> +Wed 16 Nov 2011<br /> +dataset_1.dat +</div> +</div> +<div class="summary"> +<h2>Summary</h2> +<ul> +<li><img src="tick.png" alt="[PASS]"><a href="#M0">Basic Statistics</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M1">Per base sequence quality</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M2">Per sequence quality scores</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M3">Per base sequence content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M4">Per base GC content</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M5">Per sequence GC content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M6">Per base N content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M7">Sequence Length Distribution</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M8">Sequence Duplication Levels</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M9">Overrepresented sequences</a></li> +<li><img src="error.png" alt="[FAIL]"><a href="#M10">Kmer Content</a></li> +</ul> +</div><div class="main"> -<h3>Wed 27 Apr 2011</h3> -<h3>1000gsample.fastq</h3> -<h2 id="summary">Summary</h2> -<ul> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M0">Basic Statistics</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M1">Per base sequence quality</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M2">Per sequence quality scores</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M3">Per base sequence content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M4">Per base GC content</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M5">Per sequence GC content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M6">Per base N content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M7">Sequence Length Distribution</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M8">Sequence Duplication Levels</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M9">Overrepresented sequences</a></li> -<li><img src="Icons/error.png" alt="[FAIL]"><a href="#M10">Kmer Content</a></li> -</ul> -<div class="module"><h2 id="M0"><img src="Icons/tick.png" alt="[FAIL]"> Basic Statistics</h2> +<div class="module"><h2 id="M0"><img src="tick.png" alt="[OK]"> Basic Statistics</h2><table><tr><th>Measure</th> @@ -119,7 +226,7 @@ </tr><tr><td>Filename</td> -<td>1000gsample.fastq</td> +<td>dataset_1.dat</td></tr><tr><td>File type</td> @@ -134,6 +241,10 @@ <td>5000</td></tr><tr> +<td>Filtered Sequences</td> +<td>0</td> +</tr> +<tr><td>Sequence length</td><td>54</td></tr> @@ -142,32 +253,32 @@ <td>43</td></tr></table> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M1"><img src="Icons/warning.png" alt="[FAIL]"> Per base sequence quality</h2> -<p><img class="indented" src="Images/per_base_quality.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M2"><img src="Icons/warning.png" alt="[FAIL]"> Per sequence quality scores</h2> -<p><img class="indented" src="Images/per_sequence_quality.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M3"><img src="Icons/tick.png" alt="[FAIL]"> Per base sequence content</h2> -<p><img class="indented" src="Images/per_base_sequence_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M4"><img src="Icons/tick.png" alt="[FAIL]"> Per base GC content</h2> -<p><img class="indented" src="Images/per_base_gc_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M5"><img src="Icons/warning.png" alt="[FAIL]"> Per sequence GC content</h2> -<p><img class="indented" src="Images/per_sequence_gc_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M6"><img src="Icons/tick.png" alt="[FAIL]"> Per base N content</h2> -<p><img class="indented" src="Images/per_base_n_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M7"><img src="Icons/tick.png" alt="[FAIL]"> Sequence Length Distribution</h2> -<p><img class="indented" src="Images/sequence_length_distribution.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M8"><img src="Icons/tick.png" alt="[FAIL]"> Sequence Duplication Levels</h2> -<p><img class="indented" src="Images/duplication_levels.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M9"><img src="Icons/warning.png" alt="[FAIL]"> Overrepresented sequences</h2> +</div> +<div class="module"><h2 id="M1"><img src="warning.png" alt="[WARN]"> Per base sequence quality</h2> +<p><img class="indented" src="per_base_quality.png" alt="Per base quality graph"></p> +</div> +<div class="module"><h2 id="M2"><img src="warning.png" alt="[WARN]"> Per sequence quality scores</h2> +<p><img class="indented" src="per_sequence_quality.png" alt="Per Sequence quality graph"></p> +</div> +<div class="module"><h2 id="M3"><img src="warning.png" alt="[WARN]"> Per base sequence content</h2> +<p><img class="indented" src="per_base_sequence_content.png" alt="Per base sequence content"></p> +</div> +<div class="module"><h2 id="M4"><img src="tick.png" alt="[OK]"> Per base GC content</h2> +<p><img class="indented" src="per_base_gc_content.png" alt="Per base GC content graph"></p> +</div> +<div class="module"><h2 id="M5"><img src="warning.png" alt="[WARN]"> Per sequence GC content</h2> +<p><img class="indented" src="per_sequence_gc_content.png" alt="Per sequence GC content graph"></p> +</div> +<div class="module"><h2 id="M6"><img src="tick.png" alt="[OK]"> Per base N content</h2> +<p><img class="indented" src="per_base_n_content.png" alt="N content graph"></p> +</div> +<div class="module"><h2 id="M7"><img src="tick.png" alt="[OK]"> Sequence Length Distribution</h2> +<p><img class="indented" src="sequence_length_distribution.png" alt="Sequence length distribution"></p> +</div> +<div class="module"><h2 id="M8"><img src="tick.png" alt="[OK]"> Sequence Duplication Levels</h2> +<p><img class="indented" src="duplication_levels.png" alt="Duplication level graph"></p> +</div> +<div class="module"><h2 id="M9"><img src="warning.png" alt="[WARN]"> Overrepresented sequences</h2><table><tr><th>Sequence</th> @@ -188,9 +299,9 @@ <td>Illumina Paired End PCR Primer 2 (100% over 35bp)</td></tr></table> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M10"><img src="Icons/error.png" alt="[FAIL]"> Kmer Content</h2> -<p><img class="indented" src="Images/kmer_profiles.png"></p> +</div> +<div class="module"><h2 id="M10"><img src="error.png" alt="[FAIL]"> Kmer Content</h2> +<p><img class="indented" src="kmer_profiles.png" alt="Kmer graph"></p><table><tr><th>Sequence</th> @@ -201,1132 +312,1498 @@ </tr><tr><td>CCCCC</td> -<td>1110</td> -<td>9.557241</td> -<td>23.193876</td> -<td>44</td> +<td>1180</td> +<td>9.957459</td> +<td>29.638031</td> +<td>50</td></tr><tr><td>AAAAA</td> -<td>2130</td> -<td>4.1300144</td> -<td>5.698024</td> -<td>7</td> +<td>2175</td> +<td>4.133217</td> +<td>7.129659</td> +<td>47</td></tr><tr><td>CTCCC</td> -<td>530</td> -<td>3.5749238</td> +<td>555</td> +<td>3.668942</td><td>11.56272</td><td>11</td></tr><tr><td>CCTCC</td> -<td>510</td> -<td>3.440021</td> +<td>525</td> +<td>3.4706206</td><td>11.56272</td><td>14</td></tr><tr><td>CTGGG</td><td>465</td> -<td>3.1575248</td> -<td>8.314476</td> -<td>45</td> +<td>3.0945942</td> +<td>8.331139</td> +<td>39</td> +</tr> +<tr> +<td>GGGGG</td> +<td>350</td> +<td>2.9865708</td> +<td>12.818572</td> +<td>41</td></tr><tr><td>TGGAA</td> -<td>785</td> -<td>2.929684</td> +<td>800</td> +<td>2.9261596</td><td>6.397646</td><td>17</td></tr><tr> -<td>GGGGG</td> -<td>335</td> -<td>2.9167063</td> -<td>10.660779</td> -<td>6</td> +<td>CCCAG</td> +<td>455</td> +<td>2.855999</td> +<td>9.429343</td> +<td>40</td></tr><tr><td>GAATG</td><td>775</td> -<td>2.8923633</td> +<td>2.8347175</td><td>10.053445</td><td>20</td></tr><tr> -<td>CCCAG</td> -<td>450</td> -<td>2.8820548</td> -<td>7.8420706</td> -<td>22</td> +<td>GTGTG</td> +<td>530</td> +<td>2.763172</td> +<td>7.8240557</td> +<td>33</td></tr><tr> -<td>GTGTG</td> -<td>520</td> -<td>2.7661672</td> -<td>6.513526</td> -<td>23</td> +<td>GGGAG</td> +<td>435</td> +<td>2.7487729</td> +<td>6.3220544</td> +<td>43</td></tr><tr><td>TGTGT</td> -<td>660</td> -<td>2.744307</td> +<td>670</td> +<td>2.7303638</td><td>6.109576</td><td>27</td></tr><tr> -<td>GGGAG</td> -<td>425</td> -<td>2.7401958</td> -<td>6.315732</td> -<td>6</td> -</tr> -<tr><td>ATGGA</td> -<td>730</td> -<td>2.7244196</td> +<td>735</td> +<td>2.688409</td><td>6.397646</td><td>20</td></tr><tr> -<td>GCTGG</td> -<td>395</td> -<td>2.6821985</td> -<td>6.651581</td> -<td>16</td> -</tr> -<tr> -<td>GGAGG</td> -<td>410</td> -<td>2.643483</td> -<td>7.894665</td> -<td>7</td> -</tr> -<tr><td>GGAAT</td> -<td>700</td> -<td>2.612457</td> +<td>730</td> +<td>2.6701207</td><td>7.3115954</td><td>19</td></tr><tr> +<td>GCTGG</td> +<td>400</td> +<td>2.6620166</td> +<td>8.322799</td> +<td>31</td> +</tr> +<tr> +<td>GGAGG</td> +<td>420</td> +<td>2.6539874</td> +<td>7.9104857</td> +<td>40</td> +</tr> +<tr><td>GCAGG</td> -<td>400</td> -<td>2.5732677</td> +<td>405</td> +<td>2.5535064</td><td>14.17877</td><td>16</td></tr><tr><td>CCTGG</td> -<td>370</td> -<td>2.5068476</td> +<td>375</td> +<td>2.4900866</td><td>6.6367774</td><td>7</td></tr><tr><td>CAGCC</td> -<td>380</td> -<td>2.4337354</td> -<td>6.273657</td> -<td>4</td> +<td>390</td> +<td>2.4479992</td> +<td>6.279937</td> +<td>38</td> +</tr> +<tr> +<td>GGCTG</td> +<td>365</td> +<td>2.4290898</td> +<td>9.97737</td> +<td>24</td></tr><tr><td>TGGGA</td> -<td>480</td> -<td>2.419065</td> +<td>490</td> +<td>2.4202447</td><td>7.40506</td><td>20</td></tr><tr> +<td>CCAGC</td> +<td>385</td> +<td>2.4166145</td> +<td>6.286229</td> +<td>41</td> +</tr> +<tr><td>AATGG</td> -<td>645</td> -<td>2.4071925</td> +<td>660</td> +<td>2.4140818</td><td>5.4836965</td><td>18</td></tr><tr> +<td>GCCTG</td> +<td>360</td> +<td>2.3904827</td> +<td>8.295971</td> +<td>5</td> +</tr> +<tr><td>GCCTC</td> -<td>355</td> -<td>2.3998654</td> -<td>6.622006</td> -<td>2</td> +<td>360</td> +<td>2.3851626</td> +<td>6.6286345</td> +<td>31</td></tr><tr><td>CCCTC</td> -<td>355</td> -<td>2.394524</td> -<td>8.259085</td> -<td>13</td> +<td>360</td> +<td>2.379854</td> +<td>8.267352</td> +<td>34</td></tr><tr> -<td>CCAGC</td> -<td>370</td> -<td>2.3696895</td> -<td>6.2736564</td> -<td>14</td> +<td>CTGTG</td> +<td>450</td> +<td>2.3408678</td> +<td>9.09864</td> +<td>44</td></tr><tr><td>GGAAG</td> -<td>495</td> -<td>2.3634295</td> +<td>500</td> +<td>2.3397229</td><td>14.031037</td><td>2</td></tr><tr> -<td>GGCTG</td> -<td>345</td> -<td>2.3426795</td> -<td>9.97737</td> -<td>24</td> +<td>CAGCA</td> +<td>500</td> +<td>2.32932</td> +<td>10.47649</td> +<td>14</td></tr><tr><td>CAGGA</td> -<td>490</td> -<td>2.3343499</td> +<td>495</td> +<td>2.3111706</td><td>13.99981</td><td>17</td></tr><tr> -<td>CCAGG</td> -<td>360</td> -<td>2.3107867</td> -<td>6.2876506</td> -<td>11</td> -</tr> -<tr> -<td>CTGTG</td> -<td>435</td> -<td>2.3088553</td> -<td>9.09864</td> -<td>44</td> -</tr> -<tr> -<td>GCCTG</td> -<td>340</td> -<td>2.3035896</td> -<td>8.295971</td> -<td>5</td> -</tr> -<tr><td>TCCCA</td> -<td>460</td> -<td>2.3028264</td> -<td>6.1297736</td> -<td>9</td> +<td>470</td> +<td>2.305994</td> +<td>7.370469</td> +<td>39</td></tr><tr><td>CTGCC</td> -<td>340</td> -<td>2.2984629</td> +<td>345</td> +<td>2.285781</td><td>8.277508</td><td>10</td></tr><tr> -<td>CAGCA</td> -<td>480</td> -<td>2.2816207</td> -<td>10.47649</td> -<td>14</td> +<td>GGTGG</td> +<td>340</td> +<td>2.2677608</td> +<td>5.009832</td> +<td>42</td> +</tr> +<tr> +<td>CCAGG</td> +<td>360</td> +<td>2.264732</td> +<td>6.300251</td> +<td>41</td></tr><tr><td>TTCCT</td> -<td>545</td> -<td>2.256056</td> +<td>555</td> +<td>2.2516627</td><td>7.0961456</td><td>1</td></tr><tr> +<td>TCCCC</td> +<td>335</td> +<td>2.2145865</td> +<td>8.267353</td> +<td>29</td> +</tr> +<tr> +<td>CAGGC</td> +<td>350</td> +<td>2.2018228</td> +<td>6.300251</td> +<td>42</td> +</tr> +<tr><td>CTCCT</td> -<td>415</td> -<td>2.1929073</td> +<td>425</td> +<td>2.2009897</td><td>6.4701333</td><td>15</td></tr><tr> -<td>TCCCC</td> -<td>325</td> -<td>2.1921701</td> -<td>6.6072683</td> -<td>28</td> -</tr> -<tr> -<td>CAGGC</td> -<td>335</td> -<td>2.1503155</td> -<td>6.2876506</td> -<td>14</td> +<td>GGCAG</td> +<td>340</td> +<td>2.1436844</td> +<td>6.301676</td> +<td>16</td></tr><tr><td>CCCCA</td> -<td>335</td> -<td>2.1407545</td> -<td>6.259694</td> -<td>20</td> +<td>340</td> +<td>2.129403</td> +<td>6.26596</td> +<td>31</td> +</tr> +<tr> +<td>CTCTG</td> +<td>410</td> +<td>2.1280441</td> +<td>5.1928453</td> +<td>48</td></tr><tr><td>TGGTG</td> -<td>400</td> -<td>2.127821</td> -<td>6.513526</td> -<td>9</td> +<td>405</td> +<td>2.1114805</td> +<td>6.520046</td> +<td>33</td> +</tr> +<tr> +<td>TTCCA</td> +<td>545</td> +<td>2.094778</td> +<td>6.7295837</td> +<td>33</td></tr><tr><td>CCCCT</td><td>315</td> -<td>2.1247187</td> +<td>2.0823722</td><td>6.607268</td><td>12</td></tr><tr> -<td>GGCAG</td> -<td>330</td> -<td>2.122946</td> -<td>6.301676</td> -<td>16</td> +<td>CTCAG</td> +<td>420</td> +<td>2.0652719</td> +<td>6.149596</td> +<td>46</td></tr><tr> -<td>CTCTG</td> -<td>400</td> -<td>2.1183603</td> -<td>5.187652</td> -<td>16</td> -</tr> -<tr> -<td>TTCCA</td> -<td>540</td> -<td>2.1177678</td> -<td>6.7228537</td> -<td>28</td> +<td>AGGGA</td> +<td>440</td> +<td>2.0589561</td> +<td>7.0225415</td> +<td>31</td></tr><tr><td>CAGAG</td><td>440</td> -<td>2.0961509</td> -<td>5.833255</td> -<td>28</td> +<td>2.054374</td> +<td>5.8390937</td> +<td>38</td> +</tr> +<tr> +<td>AGCAG</td> +<td>440</td> +<td>2.0543735</td> +<td>10.499857</td> +<td>15</td></tr><tr><td>CCCTG</td><td>310</td> -<td>2.095657</td> +<td>2.05389</td><td>6.622006</td><td>24</td></tr><tr> -<td>AGGGA</td> -<td>435</td> -<td>2.0769534</td> -<td>5.846266</td> -<td>1</td> -</tr> -<tr> -<td>CTCAG</td> -<td>410</td> -<td>2.0570977</td> -<td>6.143447</td> -<td>24</td> -</tr> -<tr><td>CTTCC</td> -<td>385</td> -<td>2.034384</td> +<td>390</td> +<td>2.0197318</td><td>6.4701333</td><td>17</td></tr><tr> -<td>AGCAG</td> -<td>425</td> -<td>2.0246909</td> -<td>10.499857</td> -<td>15</td> -</tr> -<tr><td>AGGAA</td> -<td>570</td> -<td>2.015381</td> +<td>580</td> +<td>2.0098667</td><td>10.390455</td><td>18</td></tr><tr> +<td>AGAGC</td> +<td>430</td> +<td>2.0076835</td> +<td>10.499858</td> +<td>5</td> +</tr> +<tr> +<td>TCTCC</td> +<td>385</td> +<td>1.9938378</td> +<td>5.181288</td> +<td>29</td> +</tr> +<tr><td>TCCTC</td> -<td>380</td> -<td>2.0079634</td> -<td>5.1761065</td> -<td>1</td> +<td>385</td> +<td>1.9938378</td> +<td>5.181288</td> +<td>48</td></tr><tr><td>TCAGC</td> -<td>400</td> -<td>2.0069244</td> +<td>405</td> +<td>1.9915122</td><td>12.286894</td><td>44</td></tr><tr> -<td>AGAGC</td> -<td>420</td> -<td>2.0008712</td> -<td>10.499858</td> -<td>5</td> +<td>TGCTG</td> +<td>380</td> +<td>1.9767327</td> +<td>6.5055346</td> +<td>47</td> +</tr> +<tr> +<td>CACCC</td> +<td>315</td> +<td>1.9728295</td> +<td>6.259694</td> +<td>9</td></tr><tr><td>TCCTG</td> -<td>375</td> -<td>1.9859626</td> +<td>380</td> +<td>1.9723336</td><td>6.4845653</td><td>8</td></tr><tr> -<td>TCTCC</td> -<td>375</td> -<td>1.9815428</td> -<td>5.1761065</td> -<td>8</td> -</tr> -<tr> -<td>CACCC</td> +<td>CAGGG</td><td>310</td> -<td>1.9809967</td> -<td>6.259694</td> -<td>9</td> -</tr> -<tr> -<td>TGTGG</td> -<td>370</td> -<td>1.9682345</td> -<td>5.210821</td> -<td>4</td> +<td>1.954536</td> +<td>6.3016763</td> +<td>21</td></tr><tr><td>GATGG</td> -<td>390</td> -<td>1.9654902</td> +<td>395</td> +<td>1.9510134</td><td>6.1708827</td><td>1</td></tr><tr><td>TGGCT</td> -<td>370</td> -<td>1.9638538</td> +<td>375</td> +<td>1.9507233</td><td>9.098641</td><td>45</td></tr><tr> -<td>TCCCT</td> -<td>370</td> -<td>1.9551222</td> -<td>5.1761065</td> -<td>37</td> -</tr> -<tr> -<td>CAGGG</td> -<td>300</td> -<td>1.9299511</td> -<td>6.3016763</td> -<td>21</td> -</tr> -<tr><td>AAGAG</td> -<td>545</td> -<td>1.9269869</td> +<td>560</td> +<td>1.9405607</td><td>9.524584</td><td>4</td></tr><tr> +<td>TGTGG</td> +<td>370</td> +<td>1.929007</td> +<td>6.5200467</td> +<td>30</td> +</tr> +<tr> +<td>CTGAG</td> +<td>390</td> +<td>1.9220302</td> +<td>6.163313</td> +<td>35</td> +</tr> +<tr> +<td>CCTGT</td> +<td>370</td> +<td>1.9204301</td> +<td>6.4845653</td> +<td>6</td> +</tr> +<tr><td>CAGAA</td> -<td>545</td> -<td>1.9226985</td> +<td>555</td> +<td>1.9189543</td><td>6.0476103</td><td>6</td></tr><tr> -<td>CTGAG</td> +<td>TCCCT</td> +<td>370</td> +<td>1.9161558</td> +<td>6.4766097</td> +<td>33</td> +</tr> +<tr> +<td>CCCAC</td> +<td>305</td> +<td>1.9101999</td> +<td>6.259694</td> +<td>4</td> +</tr> +<tr> +<td>CACCA</td> +<td>405</td> +<td>1.8825499</td> +<td>6.9757566</td> +<td>33</td> +</tr> +<tr> +<td>AAAGA</td> +<td>730</td> +<td>1.8732982</td> +<td>5.1399345</td> +<td>42</td> +</tr> +<tr> +<td>CAGTG</td><td>380</td> -<td>1.9108309</td> -<td>6.15715</td> -<td>11</td> +<td>1.8727474</td> +<td>6.163313</td> +<td>30</td> +</tr> +<tr> +<td>GAAGA</td> +<td>540</td> +<td>1.8712552</td> +<td>7.792842</td> +<td>26</td></tr><tr><td>TCTCT</td><td>460</td> -<td>1.9041945</td> +<td>1.8662432</td><td>5.068676</td><td>8</td></tr><tr> +<td>TTTCC</td> +<td>460</td> +<td>1.8662429</td> +<td>5.073749</td> +<td>38</td> +</tr> +<tr><td>GAGGC</td><td>295</td> -<td>1.897785</td> +<td>1.8599615</td><td>6.301676</td><td>22</td></tr><tr> -<td>CCCAC</td> -<td>295</td> -<td>1.885142</td> -<td>6.259694</td> -<td>4</td> +<td>TCTGT</td> +<td>455</td> +<td>1.8500755</td> +<td>5.0850673</td> +<td>49</td></tr><tr><td>CCTGC</td><td>275</td> -<td>1.8590509</td> +<td>1.8219992</td><td>9.93301</td><td>6</td></tr><tr> -<td>CCTGT</td> +<td>CCTCT</td><td>350</td> -<td>1.8535651</td> -<td>6.4845653</td> -<td>6</td> -</tr> -<tr> -<td>TTTCC</td> -<td>445</td> -<td>1.8421009</td> -<td>5.0686755</td> -<td>14</td> +<td>1.8125799</td> +<td>7.7641597</td> +<td>2</td></tr><tr><td>TGCCT</td><td>345</td> -<td>1.8270856</td> +<td>1.7906713</td><td>5.187652</td><td>12</td></tr><tr> -<td>CACAC</td> -<td>380</td> -<td>1.8022629</td> -<td>5.8073177</td> -<td>17</td> -</tr> -<tr> -<td>CCTCT</td> -<td>340</td> -<td>1.7965988</td> -<td>7.7641597</td> -<td>2</td> -</tr> -<tr><td>TTCCC</td> -<td>340</td> -<td>1.7965986</td> +<td>345</td> +<td>1.7866857</td><td>6.470133</td><td>18</td></tr><tr> -<td>GAAGA</td> -<td>500</td> -<td>1.767878</td> -<td>7.792842</td> -<td>26</td> +<td>GAGGG</td> +<td>280</td> +<td>1.769325</td> +<td>6.3283887</td> +<td>41</td> +</tr> +<tr> +<td>CACAC</td> +<td>380</td> +<td>1.7663432</td> +<td>5.813131</td> +<td>33</td> +</tr> +<tr> +<td>TCTGC</td> +<td>340</td> +<td>1.7647195</td> +<td>5.1980486</td> +<td>42</td></tr><tr><td>CTGGC</td> -<td>260</td> -<td>1.7615684</td> -<td>6.636777</td> -<td>8</td> +<td>265</td> +<td>1.7596608</td> +<td>6.6434207</td> +<td>43</td></tr><tr><td>TTCAG</td> -<td>440</td> -<td>1.7294377</td> +<td>455</td> +<td>1.7527524</td><td>9.6255</td><td>12</td></tr><tr> +<td>AGCCA</td> +<td>375</td> +<td>1.74699</td> +<td>5.8319354</td> +<td>39</td> +</tr> +<tr><td>CTCTC</td> -<td>325</td> -<td>1.717337</td> +<td>335</td> +<td>1.7348979</td><td>5.1761065</td><td>3</td></tr><tr> -<td>GTGGT</td> -<td>320</td> -<td>1.7022567</td> -<td>5.2108207</td> -<td>24</td> -</tr> -<tr><td>GGGTG</td> -<td>250</td> -<td>1.7013805</td> +<td>260</td> +<td>1.7341703</td><td>8.333022</td><td>28</td></tr><tr> -<td>TGCTT</td> -<td>410</td> -<td>1.7010024</td> -<td>5.0799813</td> -<td>4</td> +<td>TGGGG</td> +<td>260</td> +<td>1.7341703</td> +<td>8.349721</td> +<td>39</td> +</tr> +<tr> +<td>GTGGG</td> +<td>255</td> +<td>1.7008208</td> +<td>6.6730905</td> +<td>31</td> +</tr> +<tr> +<td>GGCCA</td> +<td>270</td> +<td>1.698549</td> +<td>6.293945</td> +<td>43</td> +</tr> +<tr> +<td>GCCCC</td> +<td>200</td> +<td>1.6914694</td> +<td>6.3460584</td> +<td>32</td></tr><tr><td>CTTTG</td> -<td>405</td> -<td>1.6802584</td> +<td>415</td> +<td>1.6874313</td><td>5.0799813</td><td>2</td></tr><tr> +<td>ACACA</td> +<td>485</td> +<td>1.6731915</td> +<td>5.1721287</td> +<td>14</td> +</tr> +<tr> +<td>GTGGT</td> +<td>320</td> +<td>1.6683302</td> +<td>5.216037</td> +<td>31</td> +</tr> +<tr> +<td>CTCAC</td> +<td>340</td> +<td>1.6681659</td> +<td>7.363092</td> +<td>31</td> +</tr> +<tr> +<td>TGCTT</td> +<td>410</td> +<td>1.6671008</td> +<td>5.090162</td> +<td>40</td> +</tr> +<tr> +<td>GGGGC</td> +<td>195</td> +<td>1.6602434</td> +<td>8.526694</td> +<td>40</td> +</tr> +<tr> +<td>AGTGG</td> +<td>335</td> +<td>1.654657</td> +<td>6.1708827</td> +<td>3</td> +</tr> +<tr> +<td>TTCTG</td> +<td>405</td> +<td>1.6467704</td> +<td>5.0850663</td> +<td>49</td> +</tr> +<tr><td>AGAAG</td><td>475</td> -<td>1.6794841</td> +<td>1.6460115</td><td>5.1952276</td><td>22</td></tr><tr><td>ACTCC</td> -<td>330</td> -<td>1.6520276</td> +<td>335</td> +<td>1.6436341</td><td>6.1297736</td><td>10</td></tr><tr> +<td>GGCTC</td> +<td>245</td> +<td>1.6268562</td> +<td>8.304275</td> +<td>46</td> +</tr> +<tr> +<td>TGGCA</td> +<td>330</td> +<td>1.6263331</td> +<td>8.637284</td> +<td>40</td> +</tr> +<tr> +<td>TCCTT</td> +<td>400</td> +<td>1.6228201</td> +<td>6.0946</td> +<td>40</td> +</tr> +<tr> +<td>TCTGG</td> +<td>310</td> +<td>1.612598</td> +<td>5.204428</td> +<td>43</td> +</tr> +<tr> +<td>GGGGA</td> +<td>255</td> +<td>1.6113497</td> +<td>6.3157325</td> +<td>7</td> +</tr> +<tr><td>CTGCT</td><td>310</td> -<td>1.6417291</td> +<td>1.609009</td><td>6.4845653</td><td>3</td></tr><tr> -<td>GCCCC</td> -<td>190</td> -<td>1.6395733</td> -<td>6.339712</td> -<td>37</td> +<td>CCCAA</td> +<td>345</td> +<td>1.6036536</td> +<td>5.8073177</td> +<td>10</td></tr><tr> -<td>AGTGG</td> -<td>325</td> -<td>1.6379085</td> -<td>6.1708827</td> -<td>3</td> +<td>TGGCC</td> +<td>240</td> +<td>1.5936551</td> +<td>6.6434207</td> +<td>49</td></tr><tr> -<td>TGGCA</td> -<td>325</td> -<td>1.6342632</td> -<td>6.1571493</td> -<td>16</td> -</tr> -<tr> -<td>GGCTC</td> -<td>240</td> -<td>1.626063</td> -<td>6.636776</td> -<td>25</td> -</tr> -<tr> -<td>ACACA</td> -<td>460</td> -<td>1.6192161</td> -<td>5.1721287</td> -<td>14</td> +<td>GTGCT</td> +<td>305</td> +<td>1.5865883</td> +<td>5.220104</td> +<td>50</td></tr><tr><td>GCTTT</td><td>390</td> -<td>1.6180266</td> -<td>5.0799813</td> -<td>5</td> +<td>1.5857788</td> +<td>6.1081944</td> +<td>41</td></tr><tr> -<td>TTCTG</td> -<td>390</td> -<td>1.6180266</td> -<td>5.0799813</td> -<td>3</td> +<td>CCACA</td> +<td>335</td> +<td>1.5571709</td> +<td>5.813131</td> +<td>30</td></tr><tr> -<td>TCCTT</td> -<td>390</td> -<td>1.6144258</td> -<td>6.0824113</td> -<td>16</td> +<td>CCTTC</td> +<td>300</td> +<td>1.5536399</td> +<td>6.4701333</td> +<td>17</td></tr><tr> -<td>CCCAA</td> -<td>335</td> -<td>1.588837</td> -<td>5.8073177</td> -<td>10</td> +<td>CCACT</td> +<td>315</td> +<td>1.5455065</td> +<td>6.135909</td> +<td>32</td> +</tr> +<tr> +<td>TCTTC</td> +<td>380</td> +<td>1.5416791</td> +<td>5.0737495</td> +<td>49</td> +</tr> +<tr> +<td>GTTCA</td> +<td>400</td> +<td>1.5408814</td> +<td>7.700401</td> +<td>11</td> +</tr> +<tr> +<td>AGGCA</td> +<td>330</td> +<td>1.5407803</td> +<td>5.8332543</td> +<td>6</td> +</tr> +<tr> +<td>AAAAG</td> +<td>600</td> +<td>1.5396972</td> +<td>5.782427</td> +<td>41</td></tr><tr><td>GCACA</td><td>330</td> -<td>1.5686142</td> +<td>1.5373511</td><td>5.8202715</td><td>18</td></tr><tr> -<td>GTTCA</td> -<td>395</td> -<td>1.5525635</td> -<td>7.700401</td> -<td>11</td> -</tr> -<tr> -<td>TCTTC</td> -<td>375</td> -<td>1.5523325</td> -<td>5.068676</td> -<td>4</td> -</tr> -<tr> -<td>AGGCA</td> -<td>325</td> -<td>1.5482932</td> -<td>5.8332543</td> -<td>6</td> -</tr> -<tr> -<td>GGGGA</td> -<td>240</td> -<td>1.5474048</td> -<td>6.3157325</td> -<td>7</td> -</tr> -<tr> -<td>CCTTC</td> -<td>290</td> -<td>1.5323931</td> -<td>6.4701333</td> -<td>17</td> -</tr> -<tr><td>ATGCC</td><td>305</td> -<td>1.5302798</td> +<td>1.4997808</td><td>12.286893</td><td>22</td></tr><tr><td>GAAGG</td><td>320</td> -<td>1.5278738</td> +<td>1.4974226</td><td>5.8462653</td><td>8</td></tr><tr> +<td>GAGAG</td> +<td>320</td> +<td>1.4974226</td> +<td>5.857981</td> +<td>41</td> +</tr> +<tr> +<td>TGTGC</td> +<td>285</td> +<td>1.4825499</td> +<td>5.2044287</td> +<td>29</td> +</tr> +<tr> +<td>TTGGC</td> +<td>285</td> +<td>1.4825495</td> +<td>5.199223</td> +<td>15</td> +</tr> +<tr><td>GGGAT</td> -<td>295</td> -<td>1.4867171</td> +<td>300</td> +<td>1.4817826</td><td>7.40506</td><td>21</td></tr><tr> -<td>TGTGC</td> -<td>280</td> -<td>1.4861598</td> -<td>5.199224</td> -<td>7</td> +<td>AGCTG</td> +<td>300</td> +<td>1.4784846</td> +<td>6.1633124</td> +<td>30</td></tr><tr><td>AACAG</td> -<td>420</td> -<td>1.4817125</td> +<td>425</td> +<td>1.4694693</td><td>5.1836653</td><td>10</td></tr><tr> +<td>GAGTG</td> +<td>295</td> +<td>1.4570862</td> +<td>6.1770606</td> +<td>33</td> +</tr> +<tr> +<td>GGGAC</td> +<td>230</td> +<td>1.4501395</td> +<td>6.3143044</td> +<td>40</td> +</tr> +<tr> +<td>GTGTT</td> +<td>355</td> +<td>1.4466851</td> +<td>6.134112</td> +<td>50</td> +</tr> +<tr> +<td>TTTGG</td> +<td>355</td> +<td>1.4466851</td> +<td>6.1095753</td> +<td>3</td> +</tr> +<tr><td>TCTTT</td><td>455</td> -<td>1.4755235</td> +<td>1.4461157</td><td>5.5590916</td><td>1</td></tr><tr> -<td>TTGGC</td> -<td>275</td> -<td>1.4596211</td> -<td>5.199223</td> -<td>15</td> -</tr> -<tr><td>GAGAT</td> -<td>385</td> -<td>1.4368514</td> +<td>395</td> +<td>1.4447913</td><td>6.397646</td><td>27</td></tr><tr> -<td>TTTGG</td> -<td>345</td> -<td>1.4345239</td> -<td>6.1095753</td> -<td>3</td> +<td>CAAAA</td> +<td>560</td> +<td>1.4338523</td> +<td>5.123362</td> +<td>31</td></tr><tr><td>GGTTC</td> -<td>270</td> -<td>1.4330826</td> +<td>275</td> +<td>1.4305303</td><td>10.398446</td><td>10</td></tr><tr> +<td>CCCTT</td> +<td>275</td> +<td>1.4241698</td> +<td>5.186479</td> +<td>39</td> +</tr> +<tr> +<td>CTGTT</td> +<td>350</td> +<td>1.4231348</td> +<td>5.0799813</td> +<td>10</td> +</tr> +<tr> +<td>ATGGT</td> +<td>365</td> +<td>1.4091904</td> +<td>6.7596393</td> +<td>47</td> +</tr> +<tr> +<td>TGTTG</td> +<td>345</td> +<td>1.4059336</td> +<td>5.1015162</td> +<td>40</td> +</tr> +<tr> +<td>CTGTC</td> +<td>270</td> +<td>1.4013947</td> +<td>5.198048</td> +<td>39</td> +</tr> +<tr> +<td>GAGAC</td> +<td>300</td> +<td>1.4007094</td> +<td>5.856681</td> +<td>50</td> +</tr> +<tr> +<td>CTTCT</td> +<td>345</td> +<td>1.3996824</td> +<td>7.1246448</td> +<td>50</td> +</tr> +<tr> +<td>GGCCC</td> +<td>165</td> +<td>1.398575</td> +<td>6.353853</td> +<td>2</td> +</tr> +<tr> +<td>TGAGT</td> +<td>360</td> +<td>1.3898867</td> +<td>5.7939773</td> +<td>32</td> +</tr> +<tr> +<td>GGCAC</td> +<td>220</td> +<td>1.3840029</td> +<td>6.2876506</td> +<td>17</td> +</tr> +<tr> +<td>CCTTT</td> +<td>340</td> +<td>1.3793972</td> +<td>5.068676</td> +<td>8</td> +</tr> +<tr><td>CCTTG</td><td>265</td> -<td>1.4034137</td> +<td>1.3754432</td><td>5.187652</td><td>18</td></tr><tr> -<td>CCCTT</td> -<td>265</td> -<td>1.4002901</td> -<td>5.176106</td> -<td>14</td> -</tr> -<tr> -<td>CTGTT</td> -<td>335</td> -<td>1.3898433</td> -<td>5.0799813</td> -<td>10</td> -</tr> -<tr> -<td>CCTTT</td> -<td>335</td> -<td>1.3867503</td> -<td>5.068676</td> -<td>8</td> -</tr> -<tr> -<td>GGCAC</td> -<td>215</td> -<td>1.3800533</td> -<td>6.2876506</td> -<td>17</td> -</tr> -<tr><td>TTGAA</td> -<td>465</td> -<td>1.3564935</td> +<td>475</td> +<td>1.3580486</td><td>6.4295163</td><td>7</td></tr><tr> -<td>CTTGG</td> -<td>255</td> -<td>1.3534669</td> -<td>5.1992235</td> -<td>18</td> +<td>GAGCG</td> +<td>215</td> +<td>1.3555653</td> +<td>12.603353</td> +<td>6</td></tr><tr> -<td>GTGTT</td> -<td>325</td> -<td>1.3513632</td> -<td>5.091313</td> -<td>28</td> -</tr> -<tr> -<td>GGCCC</td> -<td>155</td> -<td>1.3405302</td> -<td>6.353853</td> -<td>2</td> -</tr> -<tr> -<td>TGGTT</td> -<td>320</td> -<td>1.330573</td> -<td>5.091313</td> -<td>25</td> +<td>AAGGA</td> +<td>390</td> +<td>1.3514621</td> +<td>5.1952276</td> +<td>44</td></tr><tr><td>TTCTT</td> -<td>410</td> -<td>1.3295923</td> +<td>420</td> +<td>1.3348758</td><td>7.941558</td><td>4</td></tr><tr><td>GGGGT</td> -<td>195</td> -<td>1.327077</td> +<td>200</td> +<td>1.3339773</td><td>8.333022</td><td>45</td></tr><tr> -<td>AAGGA</td> -<td>375</td> -<td>1.3259085</td> -<td>5.1952276</td> -<td>44</td> +<td>CAGAT</td> +<td>365</td> +<td>1.3320893</td> +<td>5.4769697</td> +<td>34</td></tr><tr> -<td>CAGAT</td> -<td>350</td> -<td>1.3033215</td> -<td>5.471493</td> -<td>10</td> +<td>CTTGG</td> +<td>255</td> +<td>1.3264918</td> +<td>5.1992235</td> +<td>18</td> +</tr> +<tr> +<td>TGGTT</td> +<td>320</td> +<td>1.3040541</td> +<td>5.091313</td> +<td>25</td> +</tr> +<tr> +<td>TTGGG</td> +<td>250</td> +<td>1.3033829</td> +<td>6.5135255</td> +<td>6</td></tr><tr><td>CTGGT</td> -<td>245</td> -<td>1.3003898</td> -<td>5.1992235</td> -<td>12</td> +<td>250</td> +<td>1.3004823</td> +<td>5.204428</td> +<td>48</td> +</tr> +<tr> +<td>GCTCC</td> +<td>195</td> +<td>1.2919631</td> +<td>8.277508</td> +<td>26</td> +</tr> +<tr> +<td>TGATG</td> +<td>330</td> +<td>1.2740628</td> +<td>5.7939773</td> +<td>46</td></tr><tr><td>TGTCC</td><td>245</td> -<td>1.2974956</td> +<td>1.2716361</td><td>5.187652</td><td>21</td></tr><tr> -<td>GCTCC</td> -<td>190</td> -<td>1.2844352</td> -<td>8.277508</td> -<td>26</td> +<td>GGCTT</td> +<td>240</td> +<td>1.2484628</td> +<td>5.199223</td> +<td>4</td></tr><tr><td>GACAG</td><td>265</td> -<td>1.2624544</td> +<td>1.2372932</td><td>5.833254</td><td>27</td></tr><tr> -<td>GAGCG</td> -<td>195</td> -<td>1.2544682</td> -<td>12.603353</td> -<td>6</td> -</tr> -<tr> -<td>TTGGG</td> +<td>GGTGT</td><td>235</td> -<td>1.2500948</td> -<td>6.5135255</td> -<td>6</td> +<td>1.2251799</td> +<td>5.21082</td> +<td>27</td></tr><tr><td>AATGC</td><td>335</td> -<td>1.2474647</td> +<td>1.2226022</td><td>10.031068</td><td>21</td></tr><tr> -<td>GGCTT</td> -<td>235</td> -<td>1.2473125</td> -<td>5.199223</td> -<td>4</td> -</tr> -<tr><td>TTTGC</td> -<td>295</td> -<td>1.223892</td> +<td>300</td> +<td>1.2198299</td><td>5.0799813</td><td>9</td></tr><tr> -<td>GGTGT</td> +<td>GTCCT</td><td>230</td> -<td>1.223497</td> -<td>5.21082</td> -<td>27</td> +<td>1.1937809</td> +<td>5.1928453</td> +<td>47</td> +</tr> +<tr> +<td>GGGCC</td> +<td>140</td> +<td>1.1893166</td> +<td>6.3744006</td> +<td>43</td> +</tr> +<tr> +<td>ATCCC</td> +<td>240</td> +<td>1.1775287</td> +<td>6.135909</td> +<td>43</td> +</tr> +<tr> +<td>GCTCT</td> +<td>225</td> +<td>1.1678292</td> +<td>7.789268</td> +<td>47</td> +</tr> +<tr> +<td>AGCCC</td> +<td>185</td> +<td>1.1612303</td> +<td>6.2799363</td> +<td>31</td></tr><tr><td>GATCG</td><td>235</td> -<td>1.181698</td> -<td>6.1571493</td> -<td>45</td> +<td>1.1581463</td> +<td>6.1633124</td> +<td>29</td> +</tr> +<tr> +<td>ACCCT</td> +<td>230</td> +<td>1.128465</td> +<td>6.129773</td> +<td>10</td> +</tr> +<tr> +<td>GTTGG</td> +<td>215</td> +<td>1.1209095</td> +<td>5.2160373</td> +<td>47</td></tr><tr><td>AGCTC</td><td>225</td> -<td>1.1288949</td> +<td>1.1063956</td><td>6.1434464</td><td>25</td></tr><tr> -<td>ACCCT</td> +<td>CCCAT</td><td>225</td> -<td>1.1263824</td> +<td>1.1039332</td><td>6.129773</td> -<td>10</td> +<td>21</td></tr><tr><td>CGGAA</td><td>235</td> -<td>1.119535</td> +<td>1.0972222</td><td>9.333206</td><td>1</td></tr><tr> -<td>CCCAT</td> -<td>220</td> -<td>1.1013516</td> -<td>6.129773</td> -<td>21</td> -</tr> -<tr><td>TCTTG</td><td>265</td> -<td>1.0994283</td> +<td>1.0775164</td><td>5.0799813</td><td>21</td></tr><tr><td>ATGCA</td><td>295</td> -<td>1.0985136</td> +<td>1.0766199</td><td>5.4714913</td><td>37</td></tr><tr><td>GCTTG</td><td>205</td> -<td>1.0880812</td> +<td>1.0663953</td><td>5.199223</td><td>2</td></tr><tr><td>AGCGG</td><td>165</td> -<td>1.061473</td> +<td>1.0403174</td><td>12.603352</td><td>7</td></tr><tr> +<td>TTGCC</td> +<td>200</td> +<td>1.0380702</td> +<td>5.1876516</td> +<td>3</td> +</tr> +<tr> +<td>AACCT</td> +<td>285</td> +<td>1.0378094</td> +<td>5.4593143</td> +<td>13</td> +</tr> +<tr><td>AACCA</td><td>300</td> -<td>1.0560105</td> +<td>1.0349638</td><td>5.1721287</td><td>22</td></tr><tr> -<td>AACCT</td> -<td>280</td> -<td>1.0403365</td> -<td>5.4593143</td> -<td>13</td> -</tr> -<tr><td>CCGAG</td><td>160</td> -<td>1.0270164</td> +<td>1.0065476</td><td>12.575301</td><td>25</td></tr><tr> -<td>TTGCC</td> +<td>GTTCC</td><td>190</td> -<td>1.0062209</td> -<td>5.1876516</td> -<td>3</td> +<td>0.9861668</td> +<td>6.4845653</td> +<td>27</td></tr><tr><td>ACTCA</td> -<td>265</td> -<td>0.9846043</td> +<td>270</td> +<td>0.983188</td><td>5.4593153</td><td>11</td></tr><tr><td>CTCAT</td> -<td>250</td> -<td>0.98044825</td> +<td>255</td> +<td>0.9801258</td><td>5.7624474</td><td>4</td></tr><tr> -<td>GTTCC</td> -<td>185</td> -<td>0.9797416</td> -<td>6.4845653</td> -<td>27</td> -</tr> -<tr><td>GAACC</td> -<td>205</td> -<td>0.97444224</td> +<td>210</td> +<td>0.9783144</td><td>5.820272</td><td>25</td></tr><tr><td>GGCGG</td><td>110</td> -<td>0.9555928</td> +<td>0.93654746</td><td>10.637051</td><td>44</td></tr><tr> +<td>GCGGG</td> +<td>110</td> +<td>0.93654746</td> +<td>6.3886194</td> +<td>36</td> +</tr> +<tr> +<td>ATCGG</td> +<td>190</td> +<td>0.93637353</td> +<td>6.163312</td> +<td>30</td> +</tr> +<tr> +<td>GTCTG</td> +<td>180</td> +<td>0.9363471</td> +<td>5.2096424</td> +<td>41</td> +</tr> +<tr><td>GCGGT</td> -<td>130</td> -<td>0.8827489</td> +<td>140</td> +<td>0.93170583</td><td>13.303162</td><td>8</td></tr><tr> -<td>GCGGG</td> -<td>100</td> -<td>0.86872077</td> -<td>6.3822303</td> -<td>45</td> +<td>CGGGG</td> +<td>105</td> +<td>0.8939771</td> +<td>6.3886194</td> +<td>46</td> +</tr> +<tr> +<td>GGGCG</td> +<td>105</td> +<td>0.8939771</td> +<td>8.518159</td> +<td>43</td> +</tr> +<tr> +<td>TCGGA</td> +<td>170</td> +<td>0.83780795</td> +<td>7.395975</td> +<td>31</td> +</tr> +<tr> +<td>CTTGT</td> +<td>205</td> +<td>0.83355045</td> +<td>5.0850673</td> +<td>38</td></tr><tr><td>TGCCG</td><td>125</td> -<td>0.846908</td> +<td>0.83002883</td><td>14.93275</td><td>23</td></tr><tr><td>AGGCG</td> -<td>120</td> -<td>0.7719804</td> +<td>125</td> +<td>0.7881193</td><td>6.3016763</td><td>15</td></tr><tr><td>CGGTT</td> -<td>140</td> -<td>0.74307984</td> +<td>150</td> +<td>0.78028923</td><td>10.398446</td><td>9</td></tr><tr> +<td>GTGAC</td> +<td>150</td> +<td>0.7392424</td> +<td>6.163313</td> +<td>32</td> +</tr> +<tr><td>GCCGA</td><td>115</td> -<td>0.738168</td> +<td>0.723456</td><td>12.575301</td><td>24</td></tr><tr> +<td>CCCGC</td> +<td>85</td> +<td>0.7188745</td> +<td>6.3460584</td> +<td>30</td> +</tr> +<tr> +<td>CCCCG</td> +<td>85</td> +<td>0.7188745</td> +<td>10.576764</td> +<td>29</td> +</tr> +<tr><td>CGAGA</td> -<td>130</td> -<td>0.61931723</td> +<td>135</td> +<td>0.6303192</td><td>9.333206</td><td>26</td></tr><tr><td>CGGGA</td> -<td>85</td> -<td>0.5468194</td> +<td>90</td> +<td>0.5674459</td><td>6.301676</td><td>24</td></tr><tr><td>CACGG</td><td>85</td> -<td>0.54560244</td> +<td>0.5347284</td><td>6.2876506</td><td>37</td></tr> +<tr> +<td>CGCCT</td> +<td>80</td> +<td>0.5300361</td> +<td>6.6286345</td> +<td>30</td> +</tr> +<tr> +<td>CCGCA</td> +<td>75</td> +<td>0.47076905</td> +<td>6.2799363</td> +<td>36</td> +</tr> +<tr> +<td>CGTTG</td> +<td>40</td> +<td>0.20807713</td> +<td>5.2044277</td> +<td>46</td> +</tr></table> -<p><a href="#summary">Back to summary</a></div> -</div><div class="footer">Produced by <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC</a> (version 0.9.1)</div> -</body></html> \ No newline at end of file +</div> +</body></html><div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2"> +<tr><td><a href="dataset_1.dat_fastqc.zip">dataset_1.dat_fastqc.zip (312.4 KB)</a></td></tr> +<tr><td><a href="duplication_levels.png">duplication_levels.png (14.5 KB)</a></td></tr> +<tr><td><a href="fastqc_data.txt">fastqc_data.txt (15.0 KB)</a></td></tr> +<tr><td><a href="fastqc_report.html">fastqc_report.html (25.2 KB)</a></td></tr> +<tr><td><a href="kmer_profiles.png">kmer_profiles.png (186.7 KB)</a></td></tr> +<tr><td><a href="per_base_gc_content.png">per_base_gc_content.png (12.1 KB)</a></td></tr> +<tr><td><a href="per_base_n_content.png">per_base_n_content.png (7.4 KB)</a></td></tr> +<tr><td><a href="per_base_quality.png">per_base_quality.png (9.6 KB)</a></td></tr> +<tr><td><a href="per_base_sequence_content.png">per_base_sequence_content.png (23.9 KB)</a></td></tr> +<tr><td><a href="per_sequence_gc_content.png">per_sequence_gc_content.png (29.6 KB)</a></td></tr> +<tr><td><a href="per_sequence_quality.png">per_sequence_quality.png (21.9 KB)</a></td></tr> +<tr><td><a href="sequence_length_distribution.png">sequence_length_distribution.png (18.9 KB)</a></td></tr> +<tr><td><a href="summary.txt">summary.txt (465 B)</a></td></tr> +</table> +<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/> +FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing +</div></div><div class="footer">Produced by <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC</a> (version 0.10.0)</div> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca test-data/picard_input_sorted_pair.sam --- a/test-data/picard_input_sorted_pair.sam +++ b/test-data/picard_input_sorted_pair.sam @@ -5,11 +5,11 @@ @RG ID:rg1 SM:Z bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:2 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:3 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 141 chr2 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:4 77 chr2 50 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:4 141 chr2 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr3 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:5 141 chr3 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html @@ -6,28 +6,51 @@ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:57</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> -<b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat returned status 1 and stderr: -[Mon May 09 11:03:51 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Mon May 09 11:03:57 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=912588800 -Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 - at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) - at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:115) - at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) - at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157) - at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117) - at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) - +<b>Picard on line resources</b><ul> +<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li> +<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:22 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>5 </td></tr> +<tr class="d0"><td>PF_READS</td><td>5 </td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>0 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>0 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0 </td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0 </td></tr> +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>13 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>0 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td> + </td></tr> +</table> +<b>Picard Tool Run Log</b><hr/> +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat returned status 0 and nothing on stderr </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca test-data/picard_output_alignment_summary_metrics.html --- a/test-data/picard_output_alignment_summary_metrics.html +++ b/test-data/picard_output_alignment_summary_metrics.html @@ -12,7 +12,7 @@ </head><body><div class="document"> -Galaxy tool CollectAlignmentSummaryMetrics run at 11/05/2011 23:16:24</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr><tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> @@ -21,43 +21,38 @@ <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/><b>Picard output (transposed to make it easier to see)</b><hr/><table cellpadding="3" > -<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Wed May 11 23:16:24 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr> +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr><tr class="d1"><td>TOTAL_READS</td><td>4 </td></tr><tr class="d0"><td>PF_READS</td><td>4 </td></tr><tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr><tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr><tr class="d1"><td>PF_READS_ALIGNED</td><td>4 </td></tr><tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> -<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> +<tr class="d1"><td>PF_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> +<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228 </td></tr><tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228 </td></tr> -<tr class="d0"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> -<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> -<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> -<tr class="d1"><td>BAD_CYCLES</td><td>63 </td></tr> -<tr class="d0"><td>STRAND_BALANCE</td><td>0.25 </td></tr> -<tr class="d1"><td>PCT_CHIMERAS</td><td>0 </td></tr> -<tr class="d0"><td>PCT_ADAPTER -</td><td>0 +<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>63 </td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0.25 </td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> +<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> +<tr class="d0"><td>SAMPLE</td><td> </td></tr> +<tr class="d1"><td>LIBRARY</td><td> </td></tr> +<tr class="d0"><td>READ_GROUP +</td><td>  </td></tr></table><b>Picard Tool Run Log</b><hr/> -<pre>Wed, 11 May 2011 23:16:24 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsZJS8q6.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsZJS8q6.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetricsZJS8q6.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsZJS8q6.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. -Runtime.totalMemory()=9109504 +<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr - -Wed, 11 May 2011 23:16:24 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat returned status 0 and stderr: -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmp1-mt_l/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-11 23:16:24 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=9109504 - +INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat returned status 0 and nothing on stderr </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tool-data/shared/igv/igv_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/igv/igv_build_sites.txt.sample @@ -0,0 +1,4 @@ +#site_id site_name site_url dbkey ivg_build_name +web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum +#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum +local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -477,17 +477,6 @@ <tool file="vcf_tools/filter.xml" /><tool file="vcf_tools/extract.xml" /></section> - <section name="PacBio/Illumina Assembly" id="hybrid"> - <tool file="ilmn_pacbio/quake.xml"/> - <tool file="ilmn_pacbio/quake_pe.xml"/> - <tool file="ilmn_pacbio/soap_denovo.xml"/> - <!-- - Uncomment this tool when we support the HDF5 format - <tool file="ilmn_pacbio/smrtpipe_filter.xml"/> - --> - <tool file="ilmn_pacbio/smrtpipe_hybrid.xml"/> - <tool file="ilmn_pacbio/assembly_stats.xml"/> - </section><!-- TODO: uncomment the following EMBOSS section whenever moving to test, but comment it in .sample to eliminate diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -136,6 +136,8 @@ **Citation** +For the underlying data, please see http://genome.ucsc.edu/cite.html for the proper citation. + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_antigenic.xml --- a/tools/emboss_5/emboss_antigenic.xml +++ b/tools/emboss_5/emboss_antigenic.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_backtranseq.xml --- a/tools/emboss_5/emboss_backtranseq.xml +++ b/tools/emboss_5/emboss_backtranseq.xml @@ -219,8 +219,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_banana.xml --- a/tools/emboss_5/emboss_banana.xml +++ b/tools/emboss_5/emboss_banana.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_biosed.xml --- a/tools/emboss_5/emboss_biosed.xml +++ b/tools/emboss_5/emboss_biosed.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_btwisted.xml --- a/tools/emboss_5/emboss_btwisted.xml +++ b/tools/emboss_5/emboss_btwisted.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cai.xml --- a/tools/emboss_5/emboss_cai.xml +++ b/tools/emboss_5/emboss_cai.xml @@ -184,8 +184,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cai_custom.xml --- a/tools/emboss_5/emboss_cai_custom.xml +++ b/tools/emboss_5/emboss_cai_custom.xml @@ -26,8 +26,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_chaos.xml --- a/tools/emboss_5/emboss_chaos.xml +++ b/tools/emboss_5/emboss_chaos.xml @@ -22,8 +22,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_charge.xml --- a/tools/emboss_5/emboss_charge.xml +++ b/tools/emboss_5/emboss_charge.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_checktrans.xml --- a/tools/emboss_5/emboss_checktrans.xml +++ b/tools/emboss_5/emboss_checktrans.xml @@ -86,8 +86,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_chips.xml --- a/tools/emboss_5/emboss_chips.xml +++ b/tools/emboss_5/emboss_chips.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cirdna.xml --- a/tools/emboss_5/emboss_cirdna.xml +++ b/tools/emboss_5/emboss_cirdna.xml @@ -22,8 +22,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_codcmp.xml --- a/tools/emboss_5/emboss_codcmp.xml +++ b/tools/emboss_5/emboss_codcmp.xml @@ -329,8 +329,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_coderet.xml --- a/tools/emboss_5/emboss_coderet.xml +++ b/tools/emboss_5/emboss_coderet.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_compseq.xml --- a/tools/emboss_5/emboss_compseq.xml +++ b/tools/emboss_5/emboss_compseq.xml @@ -41,8 +41,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cpgplot.xml --- a/tools/emboss_5/emboss_cpgplot.xml +++ b/tools/emboss_5/emboss_cpgplot.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cpgreport.xml --- a/tools/emboss_5/emboss_cpgreport.xml +++ b/tools/emboss_5/emboss_cpgreport.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cusp.xml --- a/tools/emboss_5/emboss_cusp.xml +++ b/tools/emboss_5/emboss_cusp.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_cutseq.xml --- a/tools/emboss_5/emboss_cutseq.xml +++ b/tools/emboss_5/emboss_cutseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_dan.xml --- a/tools/emboss_5/emboss_dan.xml +++ b/tools/emboss_5/emboss_dan.xml @@ -83,8 +83,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_degapseq.xml --- a/tools/emboss_5/emboss_degapseq.xml +++ b/tools/emboss_5/emboss_degapseq.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_descseq.xml --- a/tools/emboss_5/emboss_descseq.xml +++ b/tools/emboss_5/emboss_descseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_diffseq.xml --- a/tools/emboss_5/emboss_diffseq.xml +++ b/tools/emboss_5/emboss_diffseq.xml @@ -63,8 +63,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_digest.xml --- a/tools/emboss_5/emboss_digest.xml +++ b/tools/emboss_5/emboss_digest.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_dotmatcher.xml --- a/tools/emboss_5/emboss_dotmatcher.xml +++ b/tools/emboss_5/emboss_dotmatcher.xml @@ -28,8 +28,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_dotpath.xml --- a/tools/emboss_5/emboss_dotpath.xml +++ b/tools/emboss_5/emboss_dotpath.xml @@ -35,8 +35,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_dottup.xml --- a/tools/emboss_5/emboss_dottup.xml +++ b/tools/emboss_5/emboss_dottup.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_dreg.xml --- a/tools/emboss_5/emboss_dreg.xml +++ b/tools/emboss_5/emboss_dreg.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_einverted.xml --- a/tools/emboss_5/emboss_einverted.xml +++ b/tools/emboss_5/emboss_einverted.xml @@ -49,8 +49,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_epestfind.xml --- a/tools/emboss_5/emboss_epestfind.xml +++ b/tools/emboss_5/emboss_epestfind.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_equicktandem.xml --- a/tools/emboss_5/emboss_equicktandem.xml +++ b/tools/emboss_5/emboss_equicktandem.xml @@ -59,8 +59,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_est2genome.xml --- a/tools/emboss_5/emboss_est2genome.xml +++ b/tools/emboss_5/emboss_est2genome.xml @@ -102,8 +102,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_etandem.xml --- a/tools/emboss_5/emboss_etandem.xml +++ b/tools/emboss_5/emboss_etandem.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_extractfeat.xml --- a/tools/emboss_5/emboss_extractfeat.xml +++ b/tools/emboss_5/emboss_extractfeat.xml @@ -97,6 +97,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_extractseq.xml --- a/tools/emboss_5/emboss_extractseq.xml +++ b/tools/emboss_5/emboss_extractseq.xml @@ -67,8 +67,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_freak.xml --- a/tools/emboss_5/emboss_freak.xml +++ b/tools/emboss_5/emboss_freak.xml @@ -35,8 +35,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_fuzznuc.xml --- a/tools/emboss_5/emboss_fuzznuc.xml +++ b/tools/emboss_5/emboss_fuzznuc.xml @@ -74,8 +74,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_fuzzpro.xml --- a/tools/emboss_5/emboss_fuzzpro.xml +++ b/tools/emboss_5/emboss_fuzzpro.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_fuzztran.xml --- a/tools/emboss_5/emboss_fuzztran.xml +++ b/tools/emboss_5/emboss_fuzztran.xml @@ -94,8 +94,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_garnier.xml --- a/tools/emboss_5/emboss_garnier.xml +++ b/tools/emboss_5/emboss_garnier.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_geecee.xml --- a/tools/emboss_5/emboss_geecee.xml +++ b/tools/emboss_5/emboss_geecee.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_getorf.xml --- a/tools/emboss_5/emboss_getorf.xml +++ b/tools/emboss_5/emboss_getorf.xml @@ -128,8 +128,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_helixturnhelix.xml --- a/tools/emboss_5/emboss_helixturnhelix.xml +++ b/tools/emboss_5/emboss_helixturnhelix.xml @@ -62,8 +62,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_hmoment.xml --- a/tools/emboss_5/emboss_hmoment.xml +++ b/tools/emboss_5/emboss_hmoment.xml @@ -31,8 +31,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_iep.xml --- a/tools/emboss_5/emboss_iep.xml +++ b/tools/emboss_5/emboss_iep.xml @@ -37,8 +37,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_infoseq.xml --- a/tools/emboss_5/emboss_infoseq.xml +++ b/tools/emboss_5/emboss_infoseq.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_isochore.xml --- a/tools/emboss_5/emboss_isochore.xml +++ b/tools/emboss_5/emboss_isochore.xml @@ -82,6 +82,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_lindna.xml --- a/tools/emboss_5/emboss_lindna.xml +++ b/tools/emboss_5/emboss_lindna.xml @@ -98,8 +98,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_marscan.xml --- a/tools/emboss_5/emboss_marscan.xml +++ b/tools/emboss_5/emboss_marscan.xml @@ -44,8 +44,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_maskfeat.xml --- a/tools/emboss_5/emboss_maskfeat.xml +++ b/tools/emboss_5/emboss_maskfeat.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_maskseq.xml --- a/tools/emboss_5/emboss_maskseq.xml +++ b/tools/emboss_5/emboss_maskseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_matcher.xml --- a/tools/emboss_5/emboss_matcher.xml +++ b/tools/emboss_5/emboss_matcher.xml @@ -56,8 +56,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_megamerger.xml --- a/tools/emboss_5/emboss_megamerger.xml +++ b/tools/emboss_5/emboss_megamerger.xml @@ -62,8 +62,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_merger.xml --- a/tools/emboss_5/emboss_merger.xml +++ b/tools/emboss_5/emboss_merger.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_msbar.xml --- a/tools/emboss_5/emboss_msbar.xml +++ b/tools/emboss_5/emboss_msbar.xml @@ -116,8 +116,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_needle.xml --- a/tools/emboss_5/emboss_needle.xml +++ b/tools/emboss_5/emboss_needle.xml @@ -125,8 +125,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_newcpgreport.xml --- a/tools/emboss_5/emboss_newcpgreport.xml +++ b/tools/emboss_5/emboss_newcpgreport.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_newcpgseek.xml --- a/tools/emboss_5/emboss_newcpgseek.xml +++ b/tools/emboss_5/emboss_newcpgseek.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_newseq.xml --- a/tools/emboss_5/emboss_newseq.xml +++ b/tools/emboss_5/emboss_newseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_noreturn.xml --- a/tools/emboss_5/emboss_noreturn.xml +++ b/tools/emboss_5/emboss_noreturn.xml @@ -30,8 +30,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_notseq.xml --- a/tools/emboss_5/emboss_notseq.xml +++ b/tools/emboss_5/emboss_notseq.xml @@ -68,8 +68,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_nthseq.xml --- a/tools/emboss_5/emboss_nthseq.xml +++ b/tools/emboss_5/emboss_nthseq.xml @@ -68,8 +68,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_octanol.xml --- a/tools/emboss_5/emboss_octanol.xml +++ b/tools/emboss_5/emboss_octanol.xml @@ -39,6 +39,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_oddcomp.xml --- a/tools/emboss_5/emboss_oddcomp.xml +++ b/tools/emboss_5/emboss_oddcomp.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_palindrome.xml --- a/tools/emboss_5/emboss_palindrome.xml +++ b/tools/emboss_5/emboss_palindrome.xml @@ -52,8 +52,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pasteseq.xml --- a/tools/emboss_5/emboss_pasteseq.xml +++ b/tools/emboss_5/emboss_pasteseq.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_patmatdb.xml --- a/tools/emboss_5/emboss_patmatdb.xml +++ b/tools/emboss_5/emboss_patmatdb.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepcoil.xml --- a/tools/emboss_5/emboss_pepcoil.xml +++ b/tools/emboss_5/emboss_pepcoil.xml @@ -45,8 +45,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepinfo.xml --- a/tools/emboss_5/emboss_pepinfo.xml +++ b/tools/emboss_5/emboss_pepinfo.xml @@ -27,8 +27,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepnet.xml --- a/tools/emboss_5/emboss_pepnet.xml +++ b/tools/emboss_5/emboss_pepnet.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepstats.xml --- a/tools/emboss_5/emboss_pepstats.xml +++ b/tools/emboss_5/emboss_pepstats.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepwheel.xml --- a/tools/emboss_5/emboss_pepwheel.xml +++ b/tools/emboss_5/emboss_pepwheel.xml @@ -44,8 +44,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepwindow.xml --- a/tools/emboss_5/emboss_pepwindow.xml +++ b/tools/emboss_5/emboss_pepwindow.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_pepwindowall.xml --- a/tools/emboss_5/emboss_pepwindowall.xml +++ b/tools/emboss_5/emboss_pepwindowall.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_plotcon.xml --- a/tools/emboss_5/emboss_plotcon.xml +++ b/tools/emboss_5/emboss_plotcon.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_plotorf.xml --- a/tools/emboss_5/emboss_plotorf.xml +++ b/tools/emboss_5/emboss_plotorf.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_polydot.xml --- a/tools/emboss_5/emboss_polydot.xml +++ b/tools/emboss_5/emboss_polydot.xml @@ -47,8 +47,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_preg.xml --- a/tools/emboss_5/emboss_preg.xml +++ b/tools/emboss_5/emboss_preg.xml @@ -20,8 +20,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_prettyplot.xml --- a/tools/emboss_5/emboss_prettyplot.xml +++ b/tools/emboss_5/emboss_prettyplot.xml @@ -112,8 +112,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_prettyseq.xml --- a/tools/emboss_5/emboss_prettyseq.xml +++ b/tools/emboss_5/emboss_prettyseq.xml @@ -52,8 +52,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_primersearch.xml --- a/tools/emboss_5/emboss_primersearch.xml +++ b/tools/emboss_5/emboss_primersearch.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_revseq.xml --- a/tools/emboss_5/emboss_revseq.xml +++ b/tools/emboss_5/emboss_revseq.xml @@ -76,8 +76,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_seqmatchall.xml --- a/tools/emboss_5/emboss_seqmatchall.xml +++ b/tools/emboss_5/emboss_seqmatchall.xml @@ -53,8 +53,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_seqret.xml --- a/tools/emboss_5/emboss_seqret.xml +++ b/tools/emboss_5/emboss_seqret.xml @@ -69,8 +69,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_showfeat.xml --- a/tools/emboss_5/emboss_showfeat.xml +++ b/tools/emboss_5/emboss_showfeat.xml @@ -122,8 +122,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_shuffleseq.xml --- a/tools/emboss_5/emboss_shuffleseq.xml +++ b/tools/emboss_5/emboss_shuffleseq.xml @@ -61,8 +61,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_sigcleave.xml --- a/tools/emboss_5/emboss_sigcleave.xml +++ b/tools/emboss_5/emboss_sigcleave.xml @@ -54,8 +54,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_sirna.xml --- a/tools/emboss_5/emboss_sirna.xml +++ b/tools/emboss_5/emboss_sirna.xml @@ -117,8 +117,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_sixpack.xml --- a/tools/emboss_5/emboss_sixpack.xml +++ b/tools/emboss_5/emboss_sixpack.xml @@ -161,8 +161,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_skipseq.xml --- a/tools/emboss_5/emboss_skipseq.xml +++ b/tools/emboss_5/emboss_skipseq.xml @@ -58,8 +58,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_splitter.xml --- a/tools/emboss_5/emboss_splitter.xml +++ b/tools/emboss_5/emboss_splitter.xml @@ -78,8 +78,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_supermatcher.xml --- a/tools/emboss_5/emboss_supermatcher.xml +++ b/tools/emboss_5/emboss_supermatcher.xml @@ -63,8 +63,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_syco.xml --- a/tools/emboss_5/emboss_syco.xml +++ b/tools/emboss_5/emboss_syco.xml @@ -196,8 +196,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_tcode.xml --- a/tools/emboss_5/emboss_tcode.xml +++ b/tools/emboss_5/emboss_tcode.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_textsearch.xml --- a/tools/emboss_5/emboss_textsearch.xml +++ b/tools/emboss_5/emboss_textsearch.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_tmap.xml --- a/tools/emboss_5/emboss_tmap.xml +++ b/tools/emboss_5/emboss_tmap.xml @@ -38,8 +38,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_tranalign.xml --- a/tools/emboss_5/emboss_tranalign.xml +++ b/tools/emboss_5/emboss_tranalign.xml @@ -83,8 +83,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_transeq.xml --- a/tools/emboss_5/emboss_transeq.xml +++ b/tools/emboss_5/emboss_transeq.xml @@ -121,8 +121,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_trimest.xml --- a/tools/emboss_5/emboss_trimest.xml +++ b/tools/emboss_5/emboss_trimest.xml @@ -91,8 +91,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_trimseq.xml --- a/tools/emboss_5/emboss_trimseq.xml +++ b/tools/emboss_5/emboss_trimseq.xml @@ -96,8 +96,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_twofeat.xml --- a/tools/emboss_5/emboss_twofeat.xml +++ b/tools/emboss_5/emboss_twofeat.xml @@ -129,8 +129,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_union.xml --- a/tools/emboss_5/emboss_union.xml +++ b/tools/emboss_5/emboss_union.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_vectorstrip.xml --- a/tools/emboss_5/emboss_vectorstrip.xml +++ b/tools/emboss_5/emboss_vectorstrip.xml @@ -81,8 +81,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_water.xml --- a/tools/emboss_5/emboss_water.xml +++ b/tools/emboss_5/emboss_water.xml @@ -65,8 +65,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_wobble.xml --- a/tools/emboss_5/emboss_wobble.xml +++ b/tools/emboss_5/emboss_wobble.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_wordcount.xml --- a/tools/emboss_5/emboss_wordcount.xml +++ b/tools/emboss_5/emboss_wordcount.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/emboss_5/emboss_wordmatch.xml --- a/tools/emboss_5/emboss_wordmatch.xml +++ b/tools/emboss_5/emboss_wordmatch.xml @@ -73,8 +73,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/fastq/fastq_groomer.xml --- a/tools/fastq/fastq_groomer.xml +++ b/tools/fastq/fastq_groomer.xml @@ -16,7 +16,7 @@ <param name="input_file" type="data" format="fastq" label="File to groom" /><param name="input_type" type="select" label="Input FASTQ quality scores type"><option value="solexa">Solexa</option> - <option value="illumina">Illumina 1.3+</option> + <option value="illumina">Illumina 1.3-1.7</option><option value="sanger" selected="True">Sanger</option><option value="cssanger">Color Space Sanger</option></param> @@ -358,6 +358,10 @@ Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format +.. class:: infomark + +Output from Illumina 1.8+ pipelines are Sanger encoded. + ------ **Citation** diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/filters/secure_hash_message_digest.xml --- a/tools/filters/secure_hash_message_digest.xml +++ b/tools/filters/secure_hash_message_digest.xml @@ -35,5 +35,11 @@ This tool outputs Secure Hashes / Message Digests of a dataset using the user selected algorithms. +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/filters/wc_gnu.xml --- a/tools/filters/wc_gnu.xml +++ b/tools/filters/wc_gnu.xml @@ -62,5 +62,11 @@ #lines words characters 7499 41376 624971 +------ + +**Citation** + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help></tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -1,4 +1,4 @@ -<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.3"> +<tool id="gatk_indel_realigner" name="Indel Realigner" version="0.0.4"><description>- perform local realignment</description><requirements><requirement type="package" version="1.2">gatk</requirement> @@ -90,7 +90,6 @@ ##start analysis specific options -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals" -p ' - -targetNotSorted ##always resort input intervals --disable_bam_indexing ' #if $analysis_param_type.analysis_param_type_selector == "advanced": diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/genetrack/genetrack_indexer.xml --- a/tools/genetrack/genetrack_indexer.xml +++ b/tools/genetrack/genetrack_indexer.xml @@ -49,10 +49,14 @@ When shifting the averaging process in GeneTrack is able correct for longer or shorter than expected fragment sizes as long as the errors are reasonably random. +See http://genetrack.bx.psu.edu/ for more information on GeneTrack. + ------ **Citation** +For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/genetrack/genetrack_peak_prediction.xml --- a/tools/genetrack/genetrack_peak_prediction.xml +++ b/tools/genetrack/genetrack_peak_prediction.xml @@ -54,10 +54,14 @@ - **Prediction method** the function used to average nearby values +See http://genetrack.bx.psu.edu/ for more information on GeneTrack. + ------ **Citation** +For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/human_genome_variation/freebayes.xml --- a/tools/human_genome_variation/freebayes.xml +++ b/tools/human_genome_variation/freebayes.xml @@ -5,11 +5,11 @@ </requirements><description>Bayesian genetic variant detector</description><command> - ln -s $reference localref.fa; - ln -s $bamfile localbam.bam; - samtools faidx localref.fa; - samtools sort localbam.bam localbam.bam; - samtools index localbam.bam; + ln -s $reference localref.fa && + ln -s $bamfile localbam.bam && + samtools faidx localref.fa 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && + samtools sort localbam.bam localbam.bam 2>&1 || echo "Error running samtools sort for FreeBayes" >&2 && + samtools index localbam.bam 2>&1 || echo "Error running samtools index for FreeBayes" >&2 && freebayes --fasta-reference localref.fa localbam.bam --vcf $output #if $params.source_select == "full": $params.showRefRepeats diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/abyss.xml --- a/tools/ilmn_pacbio/abyss.xml +++ /dev/null @@ -1,30 +0,0 @@ -<tool id="abyss" name="ABySS" version="1.0.0"> - <description>Short-read de Bruijn assembly</description> - <command interpreter="python"> - quake_wrapper.py -k $k -r $input1 -p 8 > $output1 - </command> - <inputs> - <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" /> - <param name="k" type="integer" value="16" label="Size of k-mers to correct" /> - </inputs> - <outputs> - <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" /> - </outputs> - <help> - -**What it does** - -TBD. Calls ABySS assembler - -**Parameter list** - -k - -**Output** - -Corrected reads - - </help> -</tool> - - diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/assembly_stats.py --- a/tools/ilmn_pacbio/assembly_stats.py +++ /dev/null @@ -1,83 +0,0 @@ -#!/usr/bin/env python -# -#Copyright (c) 2011, Pacific Biosciences of California, Inc. -# -#All rights reserved. -# -#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -# * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. -# -#THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY -#DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# -import sys, os -from optparse import OptionParser -from galaxy import eggs -import pkg_resources -pkg_resources.require( 'bx-python' ) -from bx.seq.fasta import FastaReader - -def getStats( fastaFile, genomeLength, minContigLength ): - lengths = [] - stats = { "Num" : 0, - "Sum" : 0, - "Max" : 0, - "Avg" : 0, - "N50" : 0, - "99%" : 0 } - fasta_reader = FastaReader( open( fastaFile, 'rb' ) ) - while True: - seq = fasta_reader.next() - if not seq: - break - if seq.length < minContigLength: - continue - lengths.append( seq.length ) - if lengths: - stats[ 'Num' ] = len( lengths ) - stats[ 'Sum' ] = sum( lengths ) - stats[ 'Max' ] = max( lengths ) - stats[ 'Avg' ] = int( sum( lengths ) / float( len( lengths ) ) ) - stats[ 'N50' ] = 0 - stats[ '99%' ] = 0 - if genomeLength == 0: - genomeLength = sum( lengths ) - lengths.sort() - lengths.reverse() - lenSum = 0 - stats[ "99%" ] = len( lengths ) - for idx, length in enumerate( lengths ): - lenSum += length - if ( lenSum > genomeLength / 2 ): - stats[ "N50" ] = length - break - lenSum = 0 - for idx, length in enumerate( lengths ): - lenSum += length - if lenSum > genomeLength * 0.99: - stats[ "99%" ] = idx + 1 - break - return stats - -def __main__(): - #Parse Command Line - usage = 'Usage: %prog input output --minContigLength' - parser = OptionParser( usage=usage ) - parser.add_option( "--minContigLength", dest="minContigLength", help="Minimum length of contigs to analyze" ) - parser.add_option( "--genomeLength", dest="genomeLength", help="Length of genome for which to calculate N50s" ) - parser.set_defaults( minContigLength=0, genomeLength=0 ) - options, args = parser.parse_args() - input_fasta_file = args[ 0 ] - output_tabular_file = args[ 1 ] - statKeys = "Num Sum Max Avg N50 99%".split( " " ) - stats = getStats( input_fasta_file, int( options.genomeLength ), int( options.minContigLength ) ) - fout = open( output_tabular_file, "w" ) - fout.write( "%s\n" % "\t".join( map( lambda key: str( stats[ key ] ), statKeys ) ) ) - fout.close() - -if __name__=="__main__": __main__() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/assembly_stats.xml --- a/tools/ilmn_pacbio/assembly_stats.xml +++ /dev/null @@ -1,54 +0,0 @@ -<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0"> - <description>Calculate common measures of assembly quality</description> - <command interpreter="python"> - assembly_stats.py $input1 $output1 --minContigLength=${minLength} - </command> - <inputs> - <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/> - <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/> - </inputs> - <outputs> - <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/> - </outputs> - <tests> - <test> - <param name="input1" value="3.fasta" ftype="fasta"/> - <param name="minLength" value="100"/> - <output name="output1" ftype="tabular" file="assembly_stats.tabular" /> - </test> - </tests> - <help> - -**What it does** - -Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50. - -**Parameter list** - -Minimum length - Only include contigs of this size or greater for calculating statistics. - -**Output** - -Num contigs - Total number of contigs in the assembly - -Sum of contig lengths - Total sum of contig lengths - -Maximum contig length - Maximum of the contig lengths - -Mean contig length - Average contig length - -N50 - Contig length at which 50% of the assembly is contained in contigs of this size or greater. - -99% - Number of contigs accounting for 99% of the observed assembly. - - </help> -</tool> - - diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/cov_model.py --- a/tools/ilmn_pacbio/cov_model.py +++ /dev/null @@ -1,238 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser, SUPPRESS_HELP -import os, random, quake - -############################################################ -# cov_model.py -# -# Given a file of kmer counts, reports the cutoff to use -# to separate trusted/untrusted kmers. -############################################################ - -############################################################ -# main -############################################################ -def main(): - usage = 'usage: %prog [options] <counts file>' - parser = OptionParser(usage) - parser.add_option('--int', dest='count_kmers', action='store_true', default=False, help='Kmers were counted as integers w/o the use of quality values [default: %default]') - parser.add_option('--ratio', dest='ratio', type='int', default=200, help='Likelihood ratio to set trusted/untrusted cutoff [default: %default]') - parser.add_option('--no_sample', dest='no_sample', action='store_true', default=False, help='Do not sample kmer coverages into kmers.txt because its already done [default: %default]') - # help='Model kmer coverage as a function of GC content of kmers [default: %default]' - parser.add_option('--gc', dest='model_gc', action='store_true', default=False, help=SUPPRESS_HELP) - (options, args) = parser.parse_args() - - if len(args) != 1: - parser.error('Must provide kmers counts file') - else: - ctsf = args[0] - - if options.count_kmers: - model_cutoff(ctsf, options.ratio) - print 'Cutoff: %s' % open('cutoff.txt').readline().rstrip() - - else: - if options.model_gc: - model_q_gc_cutoffs(ctsf, 25000, options.ratio) - else: - model_q_cutoff(ctsf, 50000, options.ratio, options.no_sample) - print 'Cutoff: %s' % open('cutoff.txt').readline().rstrip() - - -############################################################ -# model_cutoff -# -# Make a histogram of kmers to give to R to learn the cutoff -############################################################ -def model_cutoff(ctsf, ratio): - # make kmer histogram - cov_max = 0 - for line in open(ctsf): - cov = int(line.split()[1]) - if cov > cov_max: - cov_max = cov - - kmer_hist = [0]*cov_max - for line in open(ctsf): - cov = int(line.split()[1]) - kmer_hist[cov-1] += 1 - - cov_out = open('kmers.hist', 'w') - for cov in range(0,cov_max): - if kmer_hist[cov]: - print >> cov_out, '%d\t%d' % (cov+1,kmer_hist[cov]) - cov_out.close() - - os.system('R --slave --args %d < %s/cov_model.r 2> r.log' % (ratio,quake.quake_dir)) - - -############################################################ -# model_q_cutoff -# -# Sample kmers to give to R to learn the cutoff -# 'div100' is necessary when the number of kmers is too -# large for random.sample, so we only consider every 100th -# kmer. -############################################################ -def model_q_cutoff(ctsf, sample, ratio, no_sample=False): - if not no_sample: - # count number of kmer coverages - num_covs = 0 - for line in open(ctsf): - num_covs += 1 - - # choose random kmer coverages - div100 = False - if sample >= num_covs: - rand_covs = range(num_covs) - else: - if num_covs > 1000000000: - div100 = True - rand_covs = random.sample(xrange(num_covs/100), sample) - else: - rand_covs = random.sample(xrange(num_covs), sample) - rand_covs.sort() - - # print to file - out = open('kmers.txt', 'w') - kmer_i = 0 - rand_i = 0 - for line in open(ctsf): - if div100: - if kmer_i % 100 == 0 and kmer_i/100 == rand_covs[rand_i]: - print >> out, line.split()[1] - rand_i += 1 - if rand_i >= sample: - break - else: - if kmer_i == rand_covs[rand_i]: - print >> out, line.split()[1] - rand_i += 1 - if rand_i >= sample: - break - kmer_i += 1 - out.close() - - os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r.log' % (ratio,quake.quake_dir)) - - -############################################################ -# model_q_gc_cutoffs -# -# Sample kmers to give to R to learn the cutoff for each -# GC value -############################################################ -def model_q_gc_cutoffs(ctsf, sample, ratio): - # count number of kmer coverages at each at - k = len(open(ctsf).readline().split()[0]) - num_covs_at = [0]*(k+1) - for line in open(ctsf): - kmer = line.split()[0] - num_covs_at[count_at(kmer)] += 1 - - # for each AT bin - at_cutoffs = [] - for at in range(1,k): - # sample covs - if sample >= num_covs_at[at]: - rand_covs = range(num_covs_at[at]) - else: - rand_covs = random.sample(xrange(num_covs_at[at]), sample) - rand_covs.sort() - - # print to file - out = open('kmers.txt', 'w') - kmer_i = 0 - rand_i = 0 - for line in open(ctsf): - (kmer,cov) = line.split() - if count_at(kmer) == at: - if kmer_i == rand_covs[rand_i]: - print >> out, cov - rand_i += 1 - if rand_i >= sample: - break - kmer_i += 1 - out.close() - - os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r%d.log' % (ratio,quake.quake_dir,at)) - - at_cutoffs.append( open('cutoff.txt').readline().rstrip() ) - if at in [1,k-1]: # setting extremes to next closests - at_cutoffs.append( open('cutoff.txt').readline().rstrip() ) - - os.system('mv kmers.txt kmers.at%d.txt' % at) - os.system('mv cutoff.txt cutoff.at%d.txt' % at) - - out = open('cutoffs.gc.txt','w') - print >> out, '\n'.join(at_cutoffs) - out.close() - - -############################################################ -# model_q_gc_cutoffs_bigmem -# -# Sample kmers to give to R to learn the cutoff for each -# GC value -############################################################ -def model_q_gc_cutoffs_bigmem(ctsf, sample, ratio): - # input coverages - k = 0 - for line in open(ctsf): - (kmer,cov) = line.split() - if k == 0: - k = len(kmer) - at_covs = ['']*(k+1) - else: - at = count_at(kmer) - if at_covs[at]: - at_covs[at].append(cov) - else: - at_covs[at] = [cov] - - for at in range(1,k): - print '%d %d' % (at,len(at_covs[at])) - - # for each AT bin - at_cutoffs = [] - for at in range(1,k): - # sample covs - if sample >= len(at_covs[at]): - rand_covs = at_covs[at] - else: - rand_covs = random.sample(at_covs[at], sample) - - # print to file - out = open('kmers.txt', 'w') - for rc in rand_covs: - print >> out, rc - out.close() - - os.system('R --slave --args %d < %s/cov_model_qmer.r 2> r%d.log' % (ratio,quake.quake_dir,at)) - - at_cutoffs.append( open('cutoff.txt').readline().rstrip() ) - if at in [1,k-1]: # setting extremes to next closests - at_cutoffs.append( open('cutoff.txt').readline().rstrip() ) - - os.system('mv kmers.txt kmers.at%d.txt' % at) - os.system('mv cutoff.txt cutoff.at%d.txt' % at) - - out = open('cutoffs.gc.txt','w') - print >> out, '\n'.join(at_cutoffs) - out.close() - - -############################################################ -# count_at -# -# Count A's and T's in the given sequence -############################################################ -def count_at(seq): - return len([nt for nt in seq if nt in ['A','T']]) - - -############################################################ -# __main__ -############################################################ -if __name__ == '__main__': - main() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/quake.py --- a/tools/ilmn_pacbio/quake.py +++ /dev/null @@ -1,136 +0,0 @@ -#!/usr/bin/env python -from optparse import OptionParser, SUPPRESS_HELP -import os, random, sys -import cov_model - -############################################################ -# quake.py -# -# Launch pipeline to correct errors in Illumina sequencing -# reads. -############################################################ - -#r_dir = '/nfshomes/dakelley/research/error_correction/bin' -quake_dir = os.path.abspath(os.path.dirname(sys.argv[0])) - -############################################################ -# main -############################################################ -def main(): - usage = 'usage: %prog [options]' - parser = OptionParser(usage) - parser.add_option('-r', dest='readsf', help='Fastq file of reads') - parser.add_option('-f', dest='reads_listf', help='File containing fastq file names, one per line or two per line for paired end reads.') - parser.add_option('-k', dest='k', type='int', help='Size of k-mers to correct') - parser.add_option('-p', dest='proc', type='int', default=4, help='Number of processes [default: %default]') - parser.add_option('-q', dest='quality_scale', type='int', default=-1, help='Quality value ascii scale, generally 64 or 33. If not specified, it will guess.') - parser.add_option('--no_count', dest='no_count', action='store_true', default=False, help='Kmers are already counted and in expected file [reads file].qcts or [reads file].cts [default: %default]') - parser.add_option('--no_cut', dest='no_cut', action='store_true', default=False, help='Coverage model is optimized and cutoff was printed to expected file cutoff.txt [default: %default]') - parser.add_option('--int', dest='counted_kmers', action='store_true', default=False, help='Kmers were counted as integers w/o the use of quality values [default: %default]') - parser.add_option('--ratio', dest='ratio', type='int', default=200, help='Likelihood ratio to set trusted/untrusted cutoff. Generally set between 10-1000 with lower numbers suggesting a lower threshold. [default: %default]') - # help='Model kmer coverage as a function of GC content of kmers [default: %default]' - parser.add_option('--gc', dest='model_gc', action='store_true', default=False, help=SUPPRESS_HELP) - parser.add_option('--headers', action='store_true', default=False, help='Output original read headers (i.e. pass --headers to correct)' ) - (options, args) = parser.parse_args() - - if not options.readsf and not options.reads_listf: - parser.error('Must provide fastq file of reads with -r or file with list of fastq files of reads with -f') - if not options.k: - parser.error('Must provide k-mer size with -k') - if options.quality_scale == -1: - options.quality_scale = guess_quality_scale(options.readsf, options.reads_listf) - - if options.counted_kmers: - cts_suf = 'cts' - else: - cts_suf = 'qcts' - if options.readsf: - ctsf = '%s.%s' % (os.path.splitext( os.path.split(options.readsf)[1] )[0], cts_suf) - reads_str = '-r %s' % options.readsf - else: - ctsf = '%s.%s' % (os.path.split(options.reads_listf)[1], cts_suf) - reads_str = '-f %s' % options.reads_listf - - if not options.no_count and not options.no_cut: - count_kmers(options.readsf, options.reads_listf, options.k, ctsf, options.quality_scale) - - if not options.no_cut: - # model coverage - if options.counted_kmers: - cov_model.model_cutoff(ctsf, options.ratio) - else: - if options.model_gc: - cov_model.model_q_gc_cutoffs(ctsf, 10000, options.ratio) - else: - cov_model.model_q_cutoff(ctsf, 25000, options.ratio) - - - if options.model_gc: - # run correct C++ code - os.system('%s/correct %s -k %d -m %s -a cutoffs.gc.txt -p %d -q %d' % (quake_dir,reads_str, options.k, ctsf, options.proc, options.quality_scale)) - - else: - cutoff = open('cutoff.txt').readline().rstrip() - - # run correct C++ code - headers = '--headers' if options.headers else '' - os.system('%s/correct %s %s -k %d -m %s -c %s -p %d -q %d' % (quake_dir,headers, reads_str, options.k, ctsf, cutoff, options.proc, options.quality_scale)) - - -################################################################################ -# guess_quality_scale -# Guess at ascii scale of quality values by examining -# a bunch of reads and looking for quality values < 64, -# in which case we set it to 33. -################################################################################ -def guess_quality_scale(readsf, reads_listf): - reads_to_check = 1000 - if not readsf: - readsf = open(reads_listf).readline().split()[0] - - fqf = open(readsf) - reads_checked = 0 - header = fqf.readline() - while header and reads_checked < reads_to_check: - seq = fqf.readline() - mid = fqf.readline() - qual = fqf.readline().rstrip() - reads_checked += 1 - for q in qual: - if ord(q) < 64: - print 'Guessing quality values are on ascii 33 scale' - return 33 - header = fqf.readline() - - print 'Guessing quality values are on ascii 64 scale' - return 64 - - - -############################################################ -# count_kmers -# -# Count kmers in the reads file using AMOS count-kmers or -# count-qmers -############################################################ -def count_kmers(readsf, reads_listf, k, ctsf, quality_scale): - # find files - fq_files = [] - if readsf: - fq_files.append(readsf) - else: - for line in open(reads_listf): - for fqf in line.split(): - fq_files.append(fqf) - - if ctsf[-4:] == 'qcts': - os.system('cat %s | %s/count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf)) - else: - os.system('cat %s | %s/count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf)) - - -############################################################ -# __main__ -############################################################ -if __name__ == '__main__': - main() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/quake.xml --- a/tools/ilmn_pacbio/quake.xml +++ /dev/null @@ -1,44 +0,0 @@ -<tool id="quake" name="Quake" version="1.0.0"> - <description>Quality-aware error correction</description> - <command interpreter="python"> - quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1 - </command> - <inputs> - <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" /> - <param name="k" type="integer" value="16" label="Size of k-mers to correct" /> - </inputs> - <configfiles> - <configfile name="fofnfile"> -${input1.file_name} - </configfile> - </configfiles> - <outputs> - <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" /> - </outputs> - <help> - -**What it does** - -Applies the Quake_ algorithm for quality-aware correction of -substitution error in short reads. - -Kelley DR, Schatz MC, Salzberg SL. -"Quake: quality-aware detection and correction of sequencing errors." -*Genome Biol.* 2010;11(11):R116. - -.. _Quake: http://www.cbcb.umd.edu/software/quake - -**Parameter list** - -k - k-mer size for detecting spurious k-mers versus true k-mers from - the genome. Recommendations for choosing a value of k can be found - here_. - -.. _here: http://www.cbcb.umd.edu/software/quake/faq.html - -**Output** - -A FASTQ file of corrected and trimmed reads. - </help> -</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/quake_pe.xml --- a/tools/ilmn_pacbio/quake_pe.xml +++ /dev/null @@ -1,53 +0,0 @@ -<tool id="quake_pe" name="Quake PE" version="1.0.0"> - <description>Quality-aware error correction for paired-end reads</description> - <command interpreter="python"> - quake_wrapper.py --default_cutoff=$cutoff --headers -k $k -f $fofnfile -p 12 --output=$output1,$output2 - </command> - <inputs> - <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads" /> - <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads" /> - <param name="k" type="integer" value="16" label="Size of k-mers to correct" /> - <param name="cutoff" type="integer" value="0" label="Default coverage cutoff if estimation fails"/> - </inputs> - <configfiles> - <configfile name="fofnfile">${input1.file_name} ${input2.file_name} - </configfile> - </configfiles> - <outputs> - <data format="fastq" name="output1" label="Error-corrected forward reads from ${on_string}" /> - <data format="fastq" name="output2" label="Error-corrected reverse reads from ${on_string}" /> - </outputs> - <help> - -**What it does** - -Applies the Quake_ algorithm for quality-aware correction of -substitution error in short reads. This form of the tool is customized -for correcting paired-end reads. - -Kelley DR, Schatz MC, Salzberg SL. -"Quake: quality-aware detection and correction of sequencing errors." -*Genome Biol.* 2010;11(11):R116. - -.. _Quake: http://www.cbcb.umd.edu/software/quake - -**Parameter list** - -K-mer size - k-mer size for detecting spurious k-mers versus true k-mers from - the genome. Recommendations for choosing a value of k can be found - here_. - -Default coverage cutoff - If the appropriate coverage cutoff can not be found then Quake can be - forced to proceed anyways with the supplied cutoff. In this case, - the optimal cutoff can be estimated by examining - the k-mer coverage histogram by eye. - -.. _here: http://www.cbcb.umd.edu/software/quake/faq.html - -**Output** - -A FASTQ file of corrected and trimmed reads. - </help> -</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/quake_wrapper.py --- a/tools/ilmn_pacbio/quake_wrapper.py +++ /dev/null @@ -1,132 +0,0 @@ -#!/usr/bin/python -# -# Copyright (c) 2011, Pacific Biosciences of California, Inc. -# -# All rights reserved. -# -#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: -# * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. -# * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. -# -#THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED -#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY -#DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# -import sys -import os -import subprocess - -QUAKE_EXE = os.path.join( os.path.dirname(os.path.abspath(sys.argv[0])), 'quake.py' ) -cmdLine = sys.argv -cmdLine.pop(0) - -# -# horribly not robust, but it was a pain to rewrite everything with -# optparse -# -j = -1 -cut = 0 -for i,arg in enumerate(cmdLine): - if '--default_cutoff' in arg: - j = i - cut = int(arg.split('=')[1]) -if j>=0: - cmdLine = cmdLine[:j] + cmdLine[j+1:] - -j = -1 -output='' -for i,arg in enumerate(cmdLine): - if '--output' in arg: - j = i - output = arg.split('=')[1] -if j>=0: - cmdLine = cmdLine[:j] + cmdLine[j+1:] - -def backticks( cmd, merge_stderr=True ): - """ - Simulates the perl backticks (``) command with error-handling support - Returns ( command output as sequence of strings, error code, error message ) - """ - if merge_stderr: - _stderr = subprocess.STDOUT - else: - _stderr = subprocess.PIPE - - p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE, - stdout=subprocess.PIPE, stderr=_stderr, - close_fds=True ) - - out = [ l[:-1] for l in p.stdout.readlines() ] - - p.stdout.close() - if not merge_stderr: - p.stderr.close() - - # need to allow process to terminate - p.wait() - - errCode = p.returncode and p.returncode or 0 - if p.returncode>0: - errorMessage = os.linesep.join(out) - output = [] - else: - errorMessage = '' - output = out - - return output, errCode, errorMessage - -def to_stdout(): - def toCorFastq(f): - stem, ext = os.path.splitext( os.path.basename(f) ) - dir = os.path.dirname(f) - corFastq = os.path.join(dir,'%s.cor%s' % (stem,ext) ) - if not os.path.exists(corFastq): - print >>sys.stderr, "Can't find path %s" % corFastq - sys.exit(1) - return corFastq - if '-r' in cmdLine: - fastqFile = cmdLine[ cmdLine.index('-r')+1 ] - corFastq = toCorFastq(fastqFile) - infile = open( corFastq, 'r' ) - for line in infile: - sys.stdout.write( line ) - infile.close() - else: - fofnFile = cmdLine[ cmdLine.index('-f')+1 ] - infile = open(fofnFile,'r') - for line in infile: - line = line.strip() - if len(line)>0: - fastqFiles = line.split() - break - infile.close() - outs = output.split(',') - for o,f in zip(outs,fastqFiles): - cf = toCorFastq(f) - os.system( 'cp %s %s' % ( cf, o ) ) - -def run(): - cmd = '%s %s' % ( QUAKE_EXE, " ".join(cmdLine) ) - output, errCode, errMsg = backticks( cmd ) - - if errCode==0: - to_stdout() - else: - # if Quake exits with an error in cutoff determination we - # can force correction if requested - if 'cutoff.txt' in errMsg and cut>0: - outfile = open( 'cutoff.txt', 'w' ) - print >>outfile, str(cut) - outfile.close() - cmd = '%s --no_count --no_cut %s' % ( QUAKE_EXE, " ".join(cmdLine) ) - output, errCode, errMsg = backticks( cmd ) - if errCode==0: - to_stdout() - else: - print >>sys.stderr, errMsg - sys.exit(1) - -if __name__=='__main__': run() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/smrtpipe.py --- a/tools/ilmn_pacbio/smrtpipe.py +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env python -# EASY-INSTALL-SCRIPT: 'pbpy==0.1','smrtpipe.py' -__requires__ = 'pbpy==0.1' -import pkg_resources -pkg_resources.run_script('pbpy==0.1', 'smrtpipe.py') diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/smrtpipe_filter.xml --- a/tools/ilmn_pacbio/smrtpipe_filter.xml +++ /dev/null @@ -1,67 +0,0 @@ -<tool id="smrtpipe_filter" name="SMRTpipe Filter" version="1.0.0"> - <description>Produce filtered reads from a set of PacBio primary analysis outputs.</description> - <command interpreter="python"> - smrtpipe_galaxy.py --output=data/filtered_subreads.fasta --galaxy_output=${outfile} ${iniFile} - </command> - <inputs> - <conditional name="source"> - <param name="input_source" type="select" label="Choose the source for the analysis inputs"> - <option value="path">Path to fofn or multiple bas.h5 paths</option> - <option value="history">History</option> - </param> - <when value="path"> - <repeat name="inputFiles" title="Input files"> - <param name="path" type="text" label="File path" size="75"/> - </repeat> - </when> - <when value="history"> - <param name="input1" type="data" format="tabular" label="File containing input paths" /> - </when> - </conditional> - <param name="minimum_readlength" type="integer" value="50" label="Minimum raw readlength" /> - <param name="minimum_readscore" type="float" value="0.75" label="Minimum read quality" /> - </inputs> - <configfiles> - <configfile name="iniFile"> -[input] -#if $source.input_source=="history": -#for $l in open($source.input1.file_name,'r'): -$l -#end for -#else -#for $p in $source.inputFiles -${p.path} -#end for -#end if - -[S_Filter] -filters=MinRL=${minimum_readlength},MinReadScore=${minimum_readscore} - </configfile> - </configfiles> - <outputs> - <data name="outfile" format="fasta" label="Filtered subreads" /> - </outputs> - <help> - -**What it does** - -Filters PacBio bas.h5 files and produces a FASTA file of filtered subreads. - -In PacBio SMRT sequencing, the template format is a SMRTbell: a circular -molecule with adapters at two locations in the circle. The subreads are the -portions of the read between adapters. - -**Parameter list** - -Minimum readlength - Only keep reads from ZMWs that produced this many bases or more. - -Minimum read quality - Only keep reads with overall quality scores of this value or more. The read quality score is a *de novo* prediction of the accuracy of the read. - -**Output** - -FASTA file of filtered reads. - - </help> -</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/smrtpipe_galaxy.py --- a/tools/ilmn_pacbio/smrtpipe_galaxy.py +++ /dev/null @@ -1,265 +0,0 @@ -#!/usr/bin/python -import sys -import os -import subprocess -import optparse as op -import xml.etree.cElementTree as et - -TRACE=False -# -# Turn on tracing to dump out __input__.xml and __settings__.xml somewhere -# -#TRACE=True -#TRACE_PATH='/home/UNIXHOME/jsorenson' - -class SmrtpipeGalaxy: - """Wrapper for running smrtpipe under galaxy""" - def __init__( self, argv ): - self.__parseOptions( argv ) - - def __parseOptions( self, argv ): - usage = 'Usage: %prog [--help] [options] smrtpipe.ini' - parser = op.OptionParser( usage=usage, description=SmrtpipeGalaxy.__doc__ ) - parser.add_option( "--output", - help="Designate a file generated by smrtpipe as the expected output for galaxy" ) - parser.add_option( "--nproc", type="int", - help="Number of processes to use (-D NPROC)" ) - parser.add_option( "--galaxy_output", - help="File name provided by galaxy where output should be placed" ) - parser.add_option( "--dry_run", action="store_true", - help="Create auxiliary XML files and exit" ) - parser.add_option( "--dat_extension", - help="Soft link .dat files to have this extension (some pipelines require certain extensions)" ) - - parser.set_defaults( output=None, dry_run=False, galaxy_output=None, - dat_extension=None, nproc=0 ) - self.options, self.args = parser.parse_args( argv ) - - if len(self.args)!=2: - parser.error( 'Expected 1 argument' ) - - self.configFile = self.args[1] - - def __parseConfig( self ): - infile = open( self.configFile, 'r' ) - section = None - sections = [] - for line in infile: - l = line.strip() - if len(l)==0 or line.startswith('#'): - continue - if l.startswith('[') and l.endswith(']'): - section = section_factory( l[1:-1] ) - sections.append(section) - continue - if section is None: - continue - if '=' in l: - section.addParameterLine(l) - else: - section.addLine(l) - infile.close() - return sections - - def transferOutput( self ): - if not self.options.output or not self.options.galaxy_output: - return True, '' - if not os.path.exists(self.options.output): - return False, "Can't find file %s (job error?)" % self.options.output - os.system( 'cp %s %s' % (self.options.output, self.options.galaxy_output )) - return True, '' - - def run( self ): - if not os.path.exists( self.configFile ): - print >>sys.stderr, "Can't find config file %s" % self.configFile - return 1 - - sections = self.__parseConfig() - - if len(sections)==0: - print >>sys.stderr, "No sections found in %s" % self.configFile - return 1 - if sections[0].name != 'input': - print >>sys.stderr, "No [input] section found in %s" % self.configFile - return 1 - - INPUT_FILE = '__input__.xml' - SETTINGS_FILE = '__settings__.xml' - - sections[0].softLinkDats( self.options.dat_extension ) - inputXml = sections[0].makeXmlElement() - write_xml_to_file( INPUT_FILE, inputXml ) - if TRACE: - write_xml_to_file( os.path.join(TRACE_PATH,INPUT_FILE), inputXml ) - - settings = et.Element( 'smrtpipeSettings' ) - for s in sections[1:]: - s.makeXmlElement( settings ) - - write_xml_to_file( SETTINGS_FILE, settings ) - if TRACE: - write_xml_to_file( os.path.join(TRACE_PATH,SETTINGS_FILE), settings ) - - nproc = '-D NPROC=%d' % self.options.nproc if self.options.nproc>0 else '' - cmd = 'smrtpipe.py %s --params=%s xml:%s > smrtpipe.err 2>1' % \ - ( nproc, SETTINGS_FILE, INPUT_FILE ) - - if self.options.dry_run: - print 'Command to run:' - print cmd - return 0 - - out, errCode, errMsg = backticks( cmd ) - if errCode!=0: - print >>sys.stderr, "error while running: %s" % cmd - print >>sys.stderr, errMsg - if os.path.exists('log/smrtpipe.log'): - print >>sys.stderr, 'Log:' - infile = open('log/smrtpipe.log','r') - for line in infile: sys.stderr.write(line) - infile.close() - return errCode - - success, errMsg = self.transferOutput() - if not success: - print >>sys.stderr, errMsg - return 1 - - return 0 - -def write_xml_to_file( fileName, root ): - outfile = open( fileName, 'w' ) - outfile.write( '<?xml version="1.0"?>\n' ) - outfile.write( et.tostring(root) + '\n' ) - outfile.close() - -def section_factory( name ): - if name=='input': - return InputSection(name) - else: - return Section(name) - -class Section: - def __init__( self, name ): - self._name = name - self._lines = [] - self._vars = {} - - @property - def name(self): - return self._name - - def addLine( self, line ): - self._lines.append(line) - - def addParameterLine( self, line ): - self.addLine(line) - i = line.find( '=' ) - key = line[:i].strip() - value = line[i+1:].strip() - self._vars[key] = value - - def makeXmlElement( self, settings ): - if self._name=='global': - root = et.SubElement( settings, "protocol", {'name':'generic'} ) - else: - root = et.SubElement( settings, "module", {'name':self._name} ) - for k,v in self._vars.iteritems(): - param = et.SubElement( root, 'param', {'name':k} ) - val = et.SubElement( param, 'value' ) - val.text = v - return None - - def __str__( self ): - "for debugging" - buffer = [ 'S { name=' ] - buffer.append(self._name) - buffer.append('; lines=%s' % ','.join(self._lines) ) - for k,v in self._vars.iteritems(): - buffer.append('; %s=%s' % (k,v) ) - buffer.append(' }') - return ''.join(buffer) - -class InputSection( Section ): - def __init__( self, name ): - Section.__init__(self,name) - - def softLinkDats( self, newExtension ): - if not newExtension: - return - newLines = [] - for l in self._lines: - if ':' in l: - protocol = l[:l.find(':')+1] - file = l[l.find(':')+1:] - else: - protocol = '' - file = l - if os.path.exists(file) and file.endswith('.dat'): - newFile = '%s.%s' % ( file, newExtension ) - if not os.path.exists(newFile): - os.system( 'ln -s %s %s' % ( file, newFile ) ) - newLines.append(protocol+newFile) - else: - newLines.append(l) - self._lines = newLines - - def makeXmlElement( self, parent=None ): - root = et.Element( "pacbioAnalysisInputs" ) - data = et.SubElement( root, 'dataReferences' ) - iRef = 0 - for l in self._lines: - def add(x,iRef): - if len(x)==0: return iRef - node = et.SubElement( data, 'url' ) - if ':' in x: - node.attrib[ 'ref' ] = x - else: - node.attrib[ 'ref' ] = 'run:0000000-%04d' % iRef - node2 = et.SubElement( node, 'location' ) - node2.text = x - return iRef+1 - if l.endswith('fofn') and os.path.exists(l): - infile = open(l,'r') - for j,line in enumerate(infile): iRef=add(line.strip(),iRef) - infile.close() - else: - iRef=add(l,iRef) - return root - -def backticks( cmd, merge_stderr=True ): - """ - Simulates the perl backticks (``) command with error-handling support - Returns ( command output as sequence of strings, error code, error message ) - """ - if merge_stderr: - _stderr = subprocess.STDOUT - else: - _stderr = subprocess.PIPE - - p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE, - stdout=subprocess.PIPE, stderr=_stderr, - close_fds=True ) - - out = [ l[:-1] for l in p.stdout.readlines() ] - - p.stdout.close() - if not merge_stderr: - p.stderr.close() - - # need to allow process to terminate - p.wait() - - errCode = p.returncode and p.returncode or 0 - if p.returncode>0: - errorMessage = os.linesep.join(out) - output = [] - else: - errorMessage = '' - output = out - - return output, errCode, errorMessage - -if __name__=='__main__': - app = SmrtpipeGalaxy( sys.argv ) - sys.exit( app.run() ) diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/smrtpipe_hybrid.xml --- a/tools/ilmn_pacbio/smrtpipe_hybrid.xml +++ /dev/null @@ -1,59 +0,0 @@ -<tool id="smrtpipe_hybrid" name="AHA" version="1.0.0"> - <description>Assemble contigs from a set of contigs and PacBio reads.</description> - <command interpreter="python"> - smrtpipe_galaxy.py --nproc=24 --dat_extension=fasta --output=data/scaffold.fasta --galaxy_output=${outfile} ${iniFile} - </command> - <!-- - <command>cp ${iniFile} ${outfile}</command> - --> - <inputs> - <param name="contigs" format="fasta" type="data" label="Starting Contigs"/> - <param name="reads" format="fasta" type="data" label="PacBio Reads"/> - <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/> - </inputs> - <configfiles> - <configfile name="iniFile"> -[input] -assembled_contigs:${contigs} -file:${reads} - -[HybridAssembly] -instrumentModel=RS -cleanup=False -untangler=pacbio -#set $schedule2 = $schedule.replace('X',';') -paramSchedule=${schedule2} -dontFillin=False -longReadsAsStrobe=True -exactQueryIds=True -rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads -numberProcesses=16 -cluster=False -minRepeatLength=100000 - </configfile> - </configfiles> - <outputs> - <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/> - </outputs> - <help> - -**What it does** - -The AHA assembly algorithm is an AMOS_-based pipeline -for finishing bacterial-sized -genomes using draft contigs and PacBio reads. - -.. _AMOS: http://sourceforge.net/apps/mediawiki/amos - -**Parameter list** - -Parameter schedule - The parameter schedule is a semi-colon delimited list of triples. Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling). The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links. - -**Output** - -FASTA file containing scaffolded and gap-filled contigs resulting from the -hybrid assembly. - - </help> -</tool> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/ilmn_pacbio/soap_denovo.xml --- a/tools/ilmn_pacbio/soap_denovo.xml +++ /dev/null @@ -1,73 +0,0 @@ -<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0"> - <description>Short-read de novo assembly</description> - <!-- - # SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 8 -d -D - # cat ${soap_config} > ${output1} - # cp ${soap_config} ${output1} && - --> - <command> - SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R - </command> - <inputs> - <conditional name="inputs"> - <param name="read_type" type="select" label="Illumina read type"> - <option value="single">Single fragment</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/> - </when> - <when value="paired"> - <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/> - <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/> - <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" /> - </when> - </conditional> - <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" /> - </inputs> - <configfiles> - <configfile name="soap_config">max_rd_len=105 -[LIB] -#if $inputs.read_type == "single" -q=${inputs.input1.file_name} -#else -avg_ins=${inputs.d} -asm_flags=3 -reverse_seq=0 -q1=${inputs.input1.file_name} -q2=${inputs.input2.file_name} -#end if - </configfile> - </configfiles> - <outputs> - <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" /> - </outputs> - <help> - -**What it does** - -Runs SOAPdenovo_ to generate a genome assembly -using single-fragment or paired-end short reads. - -Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. -"De novo assembly of human genomes with massively parallel short read sequencing." -*Genome Res.* 2010 Feb;20(2):265-72. - -.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html - -**Parameter list** - -k - k-mer size for constructing the de Bruijn graph. The appropriate size of k is genome and data set dependent, but a good starting choice might be 75% of the read length. - -Insert size - For paired-end libraries, the expected insert size. - -**Output** - -assembly - - </help> -</tool> - - diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -112,7 +112,7 @@ <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" /><output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" /></test> - <!-- Test below gives different results on different architectures, + <!-- Test below gives different answers on different architectures, e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 slidingWinSize was fixed to be 1000, default as per readme.txt --> @@ -140,6 +140,8 @@ **Citation** +For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. <http://www.ncbi.nlm.nih.gov/pubmed/20371496>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/peak_calling/macs_wrapper.xml --- a/tools/peak_calling/macs_wrapper.xml +++ b/tools/peak_calling/macs_wrapper.xml @@ -231,6 +231,8 @@ **Citation** +For the underlying tool, please cite `Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. <http://www.ncbi.nlm.nih.gov/pubmed/18798982>`_ + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_AddOrReplaceReadGroups.xml --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -1,4 +1,4 @@ -<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1"> +<tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -1,4 +1,4 @@ -<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1"> +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -1,4 +1,4 @@ -<tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1"> +<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0"><description>creates an unaligned BAM file</description><requirements><requirement type="package">picard</requirement></requirements><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -1,4 +1,4 @@ -<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1"> +<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="1.56.0"><command interpreter="python"> picard_wrapper.py --input="$input_file" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -1,4 +1,4 @@ -<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1"> +<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_ReplaceSamHeader.xml --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -1,4 +1,4 @@ -<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1"> +<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -1,4 +1,4 @@ -<tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1"> +<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0"><description>creates a FASTQ file</description><requirements><requirement type="package">picard</requirement></requirements><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/picard_wrapper.py --- a/tools/picard/picard_wrapper.py +++ b/tools/picard/picard_wrapper.py @@ -102,7 +102,7 @@ pass tmp.close() except Exception, e: - stop_err( 'Error : %s' % str( e ) ) + stop_err( 'Read Large Exception : %s' % str( e ) ) return s def runCL(self,cl=None,output_dir=None): @@ -125,14 +125,15 @@ tef.close() stderrs = self.readLarge(temperr) stdouts = self.readLarge(templog) - if len(stderrs) > 0: + if rval > 0: s = '## executing %s returned status %d and stderr: \n%s\n' % (cl,rval,stderrs) + stdouts = '%s\n%s' % (stdouts,stderrs) else: s = '## executing %s returned status %d and nothing on stderr\n' % (cl,rval) logging.info(s) os.unlink(templog) # always os.unlink(temperr) # always - return s, stdouts # sometimes this is an output + return s, stdouts, rval # sometimes s is an output def runPic(self, jar, cl): """ @@ -141,8 +142,8 @@ runme = ['java -Xmx%s' % self.opts.maxjheap] runme.append('-jar %s' % jar) runme += cl - s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir) - return stdout + s,stdouts,rval = self.runCL(cl=runme, output_dir=self.opts.outdir) + return stdouts,rval def samToBam(self,infile=None,outdir=None): """ @@ -150,24 +151,15 @@ """ fd,tempbam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.bam') cl = ['samtools view -h -b -S -o ',tempbam,infile] - tlog,stdouts = self.runCL(cl,outdir) - return tlog,tempbam - - #def bamToSam(self,infile=None,outdir=None): - # """ - # use samtools view to convert bam to sam - # """ - # fd,tempsam = tempfile.mkstemp(dir=outdir,suffix='rgutilsTemp.sam') - # cl = ['samtools view -h -o ',tempsam,infile] - # tlog,stdouts = self.runCL(cl,outdir) - # return tlog,tempsam + tlog,stdouts,rval = self.runCL(cl,outdir) + return tlog,tempbam,rval def sortSam(self, infile=None,outfile=None,outdir=None): """ """ print '## sortSam got infile=%s,outfile=%s,outdir=%s' % (infile,outfile,outdir) cl = ['samtools sort',infile,outfile] - tlog,stdouts = self.runCL(cl,outdir) + tlog,stdouts,rval = self.runCL(cl,outdir) return tlog def cleanup(self): @@ -242,7 +234,11 @@ pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs for p in pdflist: - imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf + pbase = os.path.splitext(p)[0] # removes .pdf + imghref = '%s.jpg' % pbase + mimghref = '%s-0.jpg' % pbase # multiple pages pdf -> multiple thumbnails without asking! + if mimghref in flist: + imghref=mimghref # only one for thumbnail...it's a multi page pdf res.append('<table cellpadding="10"><tr><td>\n') res.append('<a href="%s"><img src="%s" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>\n' % (p,imghref)) res.append('</tr></td></table>\n') @@ -383,9 +379,11 @@ op.add_option('', '--taillimit', default="0") op.add_option('', '--histwidth', default="0") op.add_option('', '--minpct', default="0.01") + op.add_option('', '--malevel', default='') + op.add_option('', '--deviations', default="0.0") # CollectAlignmentSummaryMetrics op.add_option('', '--maxinsert', default="20") - op.add_option('', '--adaptors', action='append', type="string") + op.add_option('', '--adaptors', default='') # FixMateInformation and validate # CollectGcBiasMetrics op.add_option('', '--windowsize', default='100') @@ -430,7 +428,8 @@ tmp_dir = opts.outdir haveTempout = False # we use this where sam output is an option - + rval = 0 + stdouts = 'Not run yet' # set ref and dict files to use (create if necessary) ref_file_name = opts.ref if opts.ref_file <> None: @@ -453,7 +452,7 @@ pic.delme.append(dict_file_name) pic.delme.append(ref_file_name) pic.delme.append(tmp_ref_name) - s = pic.runPic(jarpath, cl) + stdouts,rval = pic.runPic(jarpath, cl) # run relevant command(s) # define temporary output @@ -486,7 +485,7 @@ cl.append('RGCN="%s"' % opts.rg_seq_center) if opts.rg_desc: cl.append('RGDS="%s"' % opts.rg_desc) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'BamIndexStats': @@ -499,9 +498,9 @@ pic.delme.append(tmp_bam_name) pic.delme.append(tmp_bai_name) pic.delme.append(tmp_name) - s = pic.runPic( opts.jar, cl ) + stdouts,rval = pic.runPic( opts.jar, cl ) f = open(pic.metricsOut,'a') - f.write(s) # got this on stdout from runCl + f.write(stdouts) # got this on stdout from runCl f.write('\n') f.close() doTranspose = False # but not transposed @@ -519,35 +518,48 @@ cl.append('READ_NAME_REGEX="%s"' % opts.readregex) if float(opts.optdupdist) > 0: cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'CollectAlignmentSummaryMetrics': - # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. + # Why do we do this fakefasta thing? + # Because we need NO fai to be available or picard barfs unless it matches the input data. # why? Dunno Seems to work without complaining if the .bai file is AWOL.... fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) try: os.symlink(ref_file_name,fakefasta) except: - s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy' + s = '## unable to symlink %s to %s - different devices? Will shutil.copy' info = s shutil.copy(ref_file_name,fakefasta) pic.delme.append(fakefasta) - cl.append('ASSUME_SORTED=%s' % opts.assumesorted) - adaptorseqs = ''.join([' ADAPTER_SEQUENCE=%s' % x for x in opts.adaptors]) - cl.append(adaptorseqs) + cl.append('ASSUME_SORTED=true') + adaptlist = opts.adaptors.split(',') + adaptorseqs = ['ADAPTER_SEQUENCE=%s' % x for x in adaptlist] + cl += adaptorseqs cl.append('IS_BISULFITE_SEQUENCED=%s' % opts.bisulphite) cl.append('MAX_INSERT_SIZE=%s' % opts.maxinsert) cl.append('OUTPUT=%s' % pic.metricsOut) cl.append('R=%s' % fakefasta) cl.append('TMP_DIR=%s' % opts.tmpdir) if not opts.assumesorted.lower() == 'true': # we need to sort input - fakeinput = '%s.sorted' % opts.input - s = pic.sortSam(opts.input, fakeinput, opts.outdir) - pic.delme.append(fakeinput) - cl.append('INPUT=%s' % fakeinput) + sortedfile = '%s.sorted' % os.path.basename(opts.input) + if opts.datatype == 'sam': # need to work with a bam + tlog,tempbam,trval = pic.samToBam(opts.input,opts.outdir) + pic.delme.append(tempbam) + try: + tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) + except: + print '## exception on sorting sam file %s' % opts.input + else: # is already bam + try: + tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) + except : # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception %s on sorting bam file %s' % (sys.exc_info()[0],opts.input) + cl.append('INPUT=%s.bam' % os.path.abspath(os.path.join(opts.outdir,sortedfile))) + pic.delme.append(os.path.join(opts.outdir,sortedfile)) else: cl.append('INPUT=%s' % os.path.abspath(opts.input)) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'CollectGcBiasMetrics': @@ -575,10 +587,10 @@ cl.append('TMP_DIR=%s' % opts.tmpdir) cl.append('CHART_OUTPUT=%s' % temppdf) cl.append('SUMMARY_OUTPUT=%s' % pic.metricsOut) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar, cl) if os.path.isfile(temppdf): cl2 = ['convert','-resize x400',temppdf,os.path.join(opts.outdir,jpgname)] # make the jpg for fixPicardOutputs to find - s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) + s,stdouts,rval = pic.runCL(cl=cl2,output_dir=opts.outdir) else: s='### runGC: Unable to find pdf %s - please check the log for the causal problem\n' % temppdf lf = open(pic.log_filename,'a') @@ -587,29 +599,40 @@ lf.close() elif pic.picname == 'CollectInsertSizeMetrics': + """ <command interpreter="python"> + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" + --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" + </command> + """ isPDF = 'InsertSizeHist.pdf' pdfpath = os.path.join(opts.outdir,isPDF) histpdf = 'InsertSizeHist.pdf' cl.append('I=%s' % opts.input) cl.append('O=%s' % pic.metricsOut) cl.append('HISTOGRAM_FILE=%s' % histpdf) - if opts.taillimit <> '0': - cl.append('TAIL_LIMIT=%s' % opts.taillimit) + #if opts.taillimit <> '0': # this was deprecated although still mentioned in the docs at 1.56 + # cl.append('TAIL_LIMIT=%s' % opts.taillimit) if opts.histwidth <> '0': cl.append('HISTOGRAM_WIDTH=%s' % opts.histwidth) if float( opts.minpct) > 0.0: cl.append('MINIMUM_PCT=%s' % opts.minpct) - pic.runPic(opts.jar,cl) + if float(opts.deviations) > 0.0: + cl.append('DEVIATIONS=%s' % opts.deviations) + if opts.malevel: + malists = opts.malevel.split(',') + malist = ['METRIC_ACCUMULATION_LEVEL=%s' % x for x in malists] + cl += malist + stdouts,rval = pic.runPic(opts.jar, cl) if os.path.exists(pdfpath): # automake thumbnail - will be added to html cl2 = ['mogrify', '-format jpg -resize x400 %s' % pdfpath] - s,stdouts = pic.runCL(cl=cl2,output_dir=opts.outdir) + pic.runCL(cl=cl2,output_dir=opts.outdir) else: s = 'Unable to find expected pdf file %s<br/>\n' % pdfpath s += 'This <b>always happens if single ended data was provided</b> to this tool,\n' s += 'so please double check that your input data really is paired-end NGS data.<br/>\n' s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n<br/>' - stdouts = '' - logging.info(s) + logging.info(s) if len(stdouts) > 0: logging.info(stdouts) @@ -627,13 +650,13 @@ cl.append('READ_NAME_REGEX="%s"' % opts.readregex) # maximum offset between two duplicate clusters cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'FixMateInformation': cl.append('I=%s' % opts.input) cl.append('O=%s' % tempout) cl.append('SORT_ORDER=%s' % opts.sortorder) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) haveTempout = True elif pic.picname == 'ReorderSam': @@ -649,14 +672,14 @@ # contig length discordance if opts.allow_contig_len_discord == 'true': cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'ReplaceSamHeader': cl.append('INPUT=%s' % opts.input) cl.append('OUTPUT=%s' % tempout) cl.append('HEADER=%s' % opts.header_file) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'CalculateHsMetrics': @@ -673,7 +696,7 @@ cl.append('INPUT=%s' % os.path.abspath(opts.input)) cl.append('OUTPUT=%s' % pic.metricsOut) cl.append('TMP_DIR=%s' % opts.tmpdir) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) elif pic.picname == 'ValidateSamFile': import pysam @@ -682,7 +705,7 @@ stf = open(pic.log_filename,'w') tlog = None if opts.datatype == 'sam': # need to work with a bam - tlog,tempbam = pic.samToBam(opts.input,opts.outdir) + tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) try: tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) except: @@ -709,7 +732,7 @@ cl.append('IS_BISULFITE_SEQUENCED=true') if opts.ref <> None or opts.ref_file <> None: cl.append('R=%s' % ref_file_name) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) if opts.datatype == 'sam': pic.delme.append(tempbam) newsam = opts.output @@ -725,10 +748,12 @@ if haveTempout: # Some Picard tools produced a potentially intermediate bam file. # Either just move to final location or create sam - shutil.move(tempout, os.path.abspath(opts.output)) - + if os.path.exists(tempout): + shutil.move(tempout, os.path.abspath(opts.output)) if opts.htmlout <> None or doFix: # return a pretty html page pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) - + if rval <> 0: + print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts) + # signal failure if __name__=="__main__": __main__() diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,7 +1,7 @@ -<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1"> +<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" - --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" + --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardFixMate.xml --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -1,4 +1,4 @@ -<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1"> +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"><description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardGCBiasMetrics.xml --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -1,4 +1,4 @@ -<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1"> +<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardHsMetrics.xml --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,4 +1,4 @@ -<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1"> +<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0"><description>for targeted resequencing data</description><command interpreter="python"> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardInsertSize.xml --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,9 +1,9 @@ -<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" - --histwidth "$histWidth" --minpct "$minPct" + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" + --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs> @@ -11,15 +11,22 @@ help="If empty, upload or import a SAM/BAM dataset."/><param name="out_prefix" value="Insertion size metrics" type="text" label="Title for the output file" help="Use this remind you what the job was for" size="120" /> - <param name="tailLimit" value="10000" type="integer" - label="Tail limit" size="5" - help="When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items" /> + <param name="deviations" value="10.0" type="float" + label="Deviations" size="5" + help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" /><param name="histWidth" value="0" type="integer" label="Histogram width" size="5" - help="Explicitly sets the histogram width, overriding the TAIL_LIMIT option - leave 0 to ignore" /> - <param name="minPct" value="0.01" type="float" + help="Explicitly sets the histogram width option - leave 0 to ignore" /> + <param name="minPct" value="0.05" type="float" label="Minimum percentage" size="5" help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" /> + <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level" + help="Level(s) at which metrics will be accumulated"> + <option value="ALL_READS" selected="true">All reads (default)</option> + <option value="SAMPLE" default="true">Sample</option> + <option value="LIBRARY" default="true">Library</option> + <option value="READ_GROUP" default="true">Read group</option> + </param></inputs><outputs><data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/> @@ -28,9 +35,10 @@ <test><param name="input_file" value="picard_input_tiny.sam" /><param name="out_prefix" value="Insertion size metrics" /> - <param name="tailLimit" value="10000" /> + <param name="deviations" value="10.0" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" /> + <param name="malevel" value="ALL_READS" /><output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" /></test></tests> diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardLibComplexity.xml --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -1,4 +1,4 @@ -<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1"> +<tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/picard/rgPicardMarkDups.xml --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -1,4 +1,4 @@ -<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1"> +<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -91,21 +91,20 @@ def fix_fastqc(self,rep=[],flist=[],runlog=[]): """ add some of our stuff to the html """ - bs = '</body></html>\n' # hope they don't change this - try: - bodyindex = rep.index(bs) # hope they don't change this - except: - bodyindex = len(rep) - 1 - res = [] - res.append('<table>\n') + bodyindex = len(rep) -1 # hope they don't change this + footrow = bodyindex - 1 + footer = rep[footrow] + rep = rep[:footrow] + rep[footrow+1:] + res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n'] flist.sort() for i,f in enumerate(flist): if not(os.path.isdir(f)): fn = os.path.split(f)[-1] res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir))) - res.append('</table><p/>\n') + res.append('</table>\n') res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n') - res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n') + res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>') + res.append(footer) fixed = rep[:bodyindex] + res + rep[bodyindex:] return fixed # with our additions @@ -147,3 +146,4 @@ f.write(''.join(html)) f.close() + diff -r b1a8b03710fed782dd80a1ac2d554dca9df2c107 -r d24b1a15ab0a61a137f024305781eb77ae4774ca tools/rgenetics/rgFastQC.xml --- a/tools/rgenetics/rgFastQC.xml +++ b/tools/rgenetics/rgFastQC.xml @@ -1,4 +1,4 @@ -<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.1"> +<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.3"><description>using FastQC from Babraham</description><command interpreter="python"> rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc https://bitbucket.org/galaxy/galaxy-central/changeset/be252c2ce6e4/ changeset: be252c2ce6e4 user: natefoo date: 2011-11-16 19:53:50 summary: Merge. affected #: 1 file diff -r d24b1a15ab0a61a137f024305781eb77ae4774ca -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -899,7 +899,9 @@ method should be removed ASAP and replaced with some properly generic and stateful way of determining link-only datasets. -nate """ - return self.tool.id == 'upload1' and self.param_dict.get( 'link_data_only', None ) == 'link_to_files' + job = self.get_job() + param_dict = job.get_param_values( self.app ) + return self.tool.id == 'upload1' and param_dict.get( 'link_data_only', None ) == 'link_to_files' def _change_ownership( self, username, gid ): job = self.get_job() https://bitbucket.org/galaxy/galaxy-central/changeset/2aa927225355/ changeset: 2aa927225355 user: natefoo date: 2011-12-08 19:22:39 summary: Actual User: Fix for newline conversion on upload, tighten file permissions for files in upload. Please make sure you clean your temp directory regularly. affected #: 5 files diff -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 -r 2aa927225355959794e75fe3649085f81a901ea9 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -95,7 +95,7 @@ fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() if in_place: - shutil.copyfile( temp_name, fname ) + shutil.move( temp_name, fname ) # Return number of lines in file. return ( i + 1, None ) else: diff -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 -r 2aa927225355959794e75fe3649085f81a901ea9 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -2,7 +2,7 @@ Galaxy Security """ -import logging, socket, operator +import logging, socket, operator, pwd from datetime import datetime, timedelta from galaxy.util.bunch import Bunch from galaxy.util import listify diff -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 -r 2aa927225355959794e75fe3649085f81a901ea9 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -282,7 +282,7 @@ # Create an empty file immediately open( data.file_name, "w" ).close() # Fix permissions - util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666) + util.umask_fix_perms( data.file_name, trans.app.config.umask, 0666 ) # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. diff -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 -r 2aa927225355959794e75fe3649085f81a901ea9 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -1,4 +1,4 @@ -import os, tempfile, StringIO +import os, tempfile, StringIO, pwd, subprocess from cgi import FieldStorage from galaxy import datatypes, util from galaxy.util.odict import odict @@ -252,6 +252,18 @@ """ Create the upload tool's JSON "param" file. """ + def _chown( path ): + try: + pwent = pwd.getpwnam( trans.user.email.split('@')[0] ) + cmd = [ '/usr/bin/sudo', '-E', trans.app.config.external_chown_script, path, pwent[0], str( pwent[3] ) ] + log.debug( 'Changing ownership of %s with: %s' % ( path, ' '.join( cmd ) ) ) + p = subprocess.Popen( cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + stdout, stderr = p.communicate() + assert p.returncode == 0, stderr + except Exception, e: + log.warning( 'Changing ownership of uploaded file %s failed: %s' % ( path, str( e ) ) ) + + # TODO: json_file should go in the working directory json_file = tempfile.mkstemp() json_file_path = json_file[1] json_file = os.fdopen( json_file[0], 'w' ) @@ -279,10 +291,8 @@ is_binary = None try: link_data_only = uploaded_dataset.link_data_only - chmod_flag = 1 except: link_data_only = 'copy_files' - chmod_flag = 0 json = dict( file_type = uploaded_dataset.file_type, ext = uploaded_dataset.ext, name = uploaded_dataset.name, @@ -292,13 +302,17 @@ is_binary = is_binary, link_data_only = link_data_only, space_to_tab = uploaded_dataset.space_to_tab, + in_place = trans.app.config.external_chown_script is None, path = uploaded_dataset.path ) - if chmod_flag == 0 and trans.app.config.drmaa_external_runjob_script: - os.chmod(uploaded_dataset.path, 0777) + # TODO: This will have to change when we start bundling inputs. + # Also, in_place above causes the file to be left behind since the + # user cannot remove it unless the parent directory is writable. + if link_data_only == 'copy_files' and trans.app.config.external_chown_script: + _chown( uploaded_dataset.path ) json_file.write( to_json_string( json ) + '\n' ) json_file.close() - if trans.app.config.drmaa_external_runjob_script: - os.chmod(json_file_path, 0777) + if trans.app.config.external_chown_script: + _chown( json_file_path ) return json_file_path def create_job( trans, params, tool, json_file_path, data_list, folder=None ): """ @@ -331,16 +345,12 @@ # Create an empty file immediately if not dataset.dataset.external_filename: open( dataset.file_name, "w" ).close() - if trans.app.config.drmaa_external_runjob_script: - os.chmod(dataset.file_name, 0777) else: for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) # Create an empty file immediately if not dataset.dataset.external_filename: open( dataset.file_name, "w" ).close() - if trans.app.config.drmaa_external_runjob_script: - os.chmod(dataset.file_name, 0777) job.state = job.states.NEW trans.sa_session.add( job ) diff -r be252c2ce6e401aa7abe2c1b1096bfedcd3eba16 -r 2aa927225355959794e75fe3649085f81a901ea9 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -80,6 +80,7 @@ converted_path = None stdout = None link_data_only = dataset.get( 'link_data_only', 'copy_files' ) + in_place = dataset.get( 'in_place', True ) try: ext = dataset.file_type @@ -161,7 +162,7 @@ os.close( fd ) gzipped_file.close() # Replace the gzipped file with the decompressed file if it's safe to do so - if dataset.type in ( 'server_dir', 'path_paste' ): + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) @@ -194,7 +195,7 @@ os.close( fd ) bzipped_file.close() # Replace the bzipped file with the decompressed file if it's safe to do so - if dataset.type in ( 'server_dir', 'path_paste' ): + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) @@ -251,7 +252,7 @@ z.close() # Replace the zipped file with the decompressed file if it's safe to do so if uncompressed is not None: - if dataset.type in ( 'server_dir', 'path_paste' ): + if dataset.type in ( 'server_dir', 'path_paste' ) or not in_place: dataset.path = uncompressed else: shutil.move( uncompressed, dataset.path ) @@ -280,7 +281,6 @@ return if data_type != 'binary': if link_data_only == 'copy_files': - in_place = True if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: in_place = False if dataset.space_to_tab: @@ -305,27 +305,18 @@ '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' file_err( err_msg, dataset, json_file ) return - if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: - # Move the dataset to its "real" path - if converted_path is not None: - shutil.copy( converted_path, output_path ) - try: - os.remove( converted_path ) - except: - pass - else: - # This should not happen, but it's here just in case - shutil.move( dataset.path, output_path ) - try: - os.chmod(output_path,0644) - except: - pass + if link_data_only == 'copy_files' and converted_path is not None: + # Move the converted dataset to its "real" path + shutil.move( converted_path, output_path ) + elif link_data_only == 'copy_files' and in_place: + # Dataset was not converted but should still be removed from original location + shutil.move( dataset.path, output_path ) elif link_data_only == 'copy_files': - shutil.move( dataset.path, output_path ) - try: - os.chmod(output_path,0644) - except: - pass + shutil.copy( dataset.path, output_path ) + + if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): + # Groom the dataset content if necessary + datatype.groom_dataset_content( output_path ) # Write the job info stdout = stdout or 'uploaded %s file' % data_type @@ -336,9 +327,7 @@ name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) - if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): - # Groom the dataset content if necessary - datatype.groom_dataset_content( output_path ) + def add_composite_file( dataset, registry, json_file, output_path, files_path ): if dataset.composite_files: os.mkdir( files_path ) @@ -396,7 +385,10 @@ add_composite_file( dataset, registry, json_file, output_path, files_path ) else: add_file( dataset, registry, json_file, output_path ) + # clean up paramfile + # TODO: this will not work when running as the actual user unless the + # parent directory is writable by the user. try: os.remove( sys.argv[3] ) except: https://bitbucket.org/galaxy/galaxy-central/changeset/4f12603141ce/ changeset: 4f12603141ce user: natefoo date: 2012-01-17 19:47:13 summary: Galaxy can now read an environment file before executing jobs on the cluster, useful if your DRM does not give you an easy way to do this directly. affected #: 5 files diff -r 2aa927225355959794e75fe3649085f81a901ea9 -r 4f12603141ce7688c197d8722231397404d7a2d9 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -109,7 +109,7 @@ self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None ) self.drmaa_external_killjob_script = kwargs.get('drmaa_external_killjob_script', None) self.external_chown_script = kwargs.get('external_chown_script', None) - self.TMPDIR = kwargs.get('TMPDIR', None) + self.environment_setup_file = kwargs.get( 'environment_setup_file', None ) self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) diff -r 2aa927225355959794e75fe3649085f81a901ea9 -r 4f12603141ce7688c197d8722231397404d7a2d9 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -733,6 +733,11 @@ def get_session_id( self ): return self.session_id + def get_env_setup_clause( self ): + if self.app.config.environment_setup_file is None: + return '' + return '[ -f "%s" ] && . %s' % ( self.app.config.environment_setup_file, self.app.config.environment_setup_file ) + def get_input_dataset_fnames( self, ds ): filenames = [] filenames = [ ds.file_name ] diff -r 2aa927225355959794e75fe3649085f81a901ea9 -r 4f12603141ce7688c197d8722231397404d7a2d9 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -52,7 +52,6 @@ %s cd %s %s -%s """ def __lineno__(): """Returns the current line number in our program.""" @@ -112,8 +111,7 @@ # external_runJob_script can be None, in which case it's not used. self.external_runJob_script = app.config.drmaa_external_runjob_script self.external_killJob_script = app.config.drmaa_external_killjob_script - self.TMPDIR = app.config.TMPDIR - self.userid = [] + self.userid = None def get_native_spec( self, url ): """Get any native DRM arguments specified by the site configuration""" @@ -176,26 +174,22 @@ native_spec = self.get_native_spec( runner_url ) if native_spec is not None: jt.nativeSpecification = native_spec - #set and export galaxy user PATH enviroment to actual user if submitting jobs as actual user + + # fill in the DRM's job run template + script = drm_template % ( job_wrapper.galaxy_lib_dir, + job_wrapper.get_env_setup_clause(), + os.path.abspath( job_wrapper.working_directory ), + command_line ) + try: - if self.external_runJob_script: - export_path = 'export PATH=%s:$PATH' %(os.environ['PATH']) - else: - export_path = '' + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0755 ) except: - export_path = '' - - if self.TMPDIR: - export_tmp = 'export TMPDIR=%s' %self.TMPDIR - else: - export_tmp = '' - - script = drm_template % ( job_wrapper.galaxy_lib_dir, export_path, os.path.abspath( job_wrapper.working_directory ), export_tmp, command_line ) - - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0755 ) + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception( "failure running job %s" % job_wrapper.get_id_tag() ) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: diff -r 2aa927225355959794e75fe3649085f81a901ea9 -r 4f12603141ce7688c197d8722231397404d7a2d9 lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -42,6 +42,7 @@ export PYTHONPATH="$GALAXY_LIB" fi fi +%s cd %s %s """ @@ -61,6 +62,7 @@ [ ! -d $dir ] && mkdir -p $dir [ ! -e $dataset ] && ln -s %s/$file $dataset done +%s cd %s %s """ @@ -265,9 +267,17 @@ # write the job script if self.app.config.pbs_stage_path != '': - script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + output_files), self.app.config.pbs_stage_path, exec_dir, command_line) + script = pbs_symlink_template % ( job_wrapper.galaxy_lib_dir, + " ".join( job_wrapper.get_input_fnames() + output_files ), + self.app.config.pbs_stage_path, + job_wrapper.get_env_setup_clause(), + exec_dir, + command_line ) else: - script = pbs_template % ( job_wrapper.galaxy_lib_dir, exec_dir, command_line ) + script = pbs_template % ( job_wrapper.galaxy_lib_dir, + job_wrapper.get_env_setup_clause(), + exec_dir, + command_line ) job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id) fh = file(job_file, "w") fh.write(script) diff -r 2aa927225355959794e75fe3649085f81a901ea9 -r 4f12603141ce7688c197d8722231397404d7a2d9 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -551,29 +551,27 @@ # currently available are 'pbs' and 'drmaa'. #start_job_runners = None -# Uncomment drmaa_external_runjob_script , drmaa_external_killjob_script, and external_chown_script pameters and have them point to the -# absolute path for scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py. -# The scripts directory is located in the top level galaxy directory. The parameters when -# uncommented allow for submission to the drmaa queue with the user name of the user submitting -# the job and not the galaxy user. In order for this to work the actual user must log into galaxy -# and the galaxy authentication must be consistent with the authentication on the server in which the -# drmaa queue is running (i.e. the username must have an account on the server and be allowed to -# submit jobs to the queue). The galaxy user must also be given sudo permission to execute -# scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py in /etc/sudoers -# Example: -# galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_runner.py -# galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_killer.py -# Also the -# Defaults requiretty -# in /etc/sudoers must be commented out +# For sites where all users in Galaxy match users on the system on which Galaxy +# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the +# actual user instead of as the user running the Galaxy server process. For +# details on these options, see the documentation at: +# +# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster +# #drmaa_external_runjob_script = scripts/drmaa_external_runner.py #drmaa_external_killjob_script = scripts/drmaa_external_killer.py #external_chown_script = scripts/external_chown_script.py -#important if running as actual user since enviromental variables are not passed -#will supercede an other definition of TMPDIR if using drmaa -#TMPDIR = /opt/galaxy/database/tmp - +# File to source to set up the environment when running jobs. By default, the +# environment in which the Galaxy server starts is used when running jobs +# locally, and the environment set up per the DRM's submission method and +# policy is used when running jobs on a cluster (try testing with `qsub` on the +# command line). environment_setup_file can be set to the path of a file on +# the cluster that should be sourced by the user to set up the environment +# prior to running tools. This can be especially useful for running jobs as +# the actual user, to remove the need to configure each user's environment +# individually. This only affects cluster jobs, not local jobs. +#environment_setup_file = None # The URL for the default runner to use when a tool doesn't explicitly define a # runner below. https://bitbucket.org/galaxy/galaxy-central/changeset/419260098a6f/ changeset: 419260098a6f user: natefoo date: 2012-01-18 16:34:39 summary: Merge galaxy-central. affected #: 396 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/7c3c50784374/ changeset: 7c3c50784374 user: natefoo date: 2012-01-18 20:34:00 summary: A bit more actual user cleaning. affected #: 6 files diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -589,3 +589,4 @@ os.write( fd, '</sniffers>\n' ) os.write( fd, '</datatypes>\n' ) os.close( fd ) + os.chmod( self.xml_filename, 0644 ) diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -2,7 +2,7 @@ Galaxy Security """ -import logging, socket, operator, pwd +import logging, socket, operator from datetime import datetime, timedelta from galaxy.util.bunch import Bunch from galaxy.util import listify diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -30,8 +30,6 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify -from galaxy.web import security -import socket from galaxy.visualization.tracks.visual_analytics import TracksterConfig @@ -1637,13 +1635,13 @@ DatasetFilenameWrapper( converted_dataset, datatypes_registry = self.app.datatypes_registry, tool = Bunch( conversion_name = Bunch( extensions = conv_ext ) ), - name = conversion_name, config_info = self.app.config ) + name = conversion_name ) # Wrap actual input dataset input_values[ input.name ] = \ DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, tool = self, - name = input.name, config_info = self.app.config ) + name = input.name ) elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app, other_values = param_dict ) @@ -1681,28 +1679,28 @@ param_dict[name] = DatasetFilenameWrapper( data, datatypes_registry = self.app.datatypes_registry, tool = self, - name = name, config_info = self.app.config ) + name = name ) if data: for child in data.children: - param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child,config_info = self.app.config ) + param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for name, hda in output_datasets.items(): # Write outputs to the working directory (for security purposes) # if desired. if self.app.config.outputs_to_working_directory: try: false_path = [ dp.false_path for dp in output_paths if dp.real_path == hda.file_name ][0] - param_dict[name] = DatasetFilenameWrapper( hda, false_path = false_path, config_info = self.app.config ) + param_dict[name] = DatasetFilenameWrapper( hda, false_path = false_path ) open( false_path, 'w' ).close() except IndexError: log.warning( "Unable to determine alternate path for writing job outputs, outputs will be written to their real paths" ) - param_dict[name] = DatasetFilenameWrapper( hda, config_info = self.app.config ) + param_dict[name] = DatasetFilenameWrapper( hda ) else: - param_dict[name] = DatasetFilenameWrapper( hda, config_info = self.app.config ) + param_dict[name] = DatasetFilenameWrapper( hda ) # Provide access to a path to store additional files # TODO: path munging for cluster/dataset server relocatability param_dict[name].files_path = os.path.abspath(os.path.join( job_working_directory, "dataset_%s_files" % (hda.dataset.id) )) for child in hda.children: - param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child, config_info = self.app.config ) + param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for out_name, output in self.outputs.iteritems(): if out_name not in param_dict and output.filters: # Assume the reason we lack this output is because a filter @@ -2294,7 +2292,7 @@ def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) - def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None , config_info=None): + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None ): if not dataset: try: # TODO: allow this to work when working with grouping @@ -2306,14 +2304,6 @@ self.dataset = dataset self.metadata = self.MetadataWrapper( dataset.metadata ) self.false_path = false_path - - # create web_display_url attribute - sec = security.SecurityHelper( id_secret=config_info.id_secret ) - try: - url = 'http://' + socket.getfqdn() + config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) + '/display/?preview=True' - self.web_display_url = url - except: - self.web_display_url = None def __str__( self ): if self.false_path is not None: diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -149,7 +149,7 @@ galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = trans.app.datatypes_registry, tool = tool, - name = input.name, config_info = trans.app.config) + name = input.name ) elif isinstance( input, SelectToolParameter ): input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) else: diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 tools/data_source/upload.py --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -305,19 +305,19 @@ '<b>Copy files into Galaxy</b> instead of <b>Link to files without copying into Galaxy</b> so grooming can be performed.' file_err( err_msg, dataset, json_file ) return - if link_data_only == 'copy_files' and converted_path is not None: - # Move the converted dataset to its "real" path - shutil.move( converted_path, output_path ) - elif link_data_only == 'copy_files' and in_place: - # Dataset was not converted but should still be removed from original location + if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: + # Move the dataset to its "real" path + if converted_path is not None: + shutil.copy( converted_path, output_path ) + try: + os.remove( converted_path ) + except: + pass + else: + # This should not happen, but it's here just in case + shutil.copy( dataset.path, output_path ) + elif link_data_only == 'copy_files': shutil.move( dataset.path, output_path ) - elif link_data_only == 'copy_files': - shutil.copy( dataset.path, output_path ) - - if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): - # Groom the dataset content if necessary - datatype.groom_dataset_content( output_path ) - # Write the job info stdout = stdout or 'uploaded %s file' % data_type info = dict( type = 'dataset', @@ -328,6 +328,10 @@ line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) + if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): + # Groom the dataset content if necessary + datatype.groom_dataset_content( output_path ) + def add_composite_file( dataset, registry, json_file, output_path, files_path ): if dataset.composite_files: os.mkdir( files_path ) diff -r 419260098a6f394eb44b890b9740a08ff9574c36 -r 7c3c507843740ce7cb766c11559bde58fdcc7916 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -640,6 +640,7 @@ # run with the runner defined with default_cluster_job_runner. [galaxy:tool_runners] + biomart = local:/// encode_db1 = local:/// hbvar = local:/// https://bitbucket.org/galaxy/galaxy-central/changeset/e250efd2a19c/ changeset: e250efd2a19c user: natefoo date: 2012-01-18 20:34:27 summary: Merge galaxy-central. affected #: 34 files diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -156,7 +156,7 @@ dict of tool parameter values. """ param_dict = dict( [ ( p.name, p.value ) for p in self.parameters ] ) - tool = app.toolbox.tools_by_id[self.tool_id] + tool = app.toolbox.get_tool( self.tool_id ) param_dict = tool.params_from_strings( param_dict, app, ignore_errors=ignore_errors ) return param_dict def check_if_output_datasets_deleted( self ): @@ -228,7 +228,7 @@ dict of tool parameter values. """ param_dict = dict( [ ( p.name, p.value ) for p in self.parent_job.parameters ] ) - tool = app.toolbox.tools_by_id[self.tool_id] + tool = app.toolbox.get_tool( self.tool_id ) param_dict = tool.params_from_strings( param_dict, app ) return param_dict diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -4,6 +4,7 @@ shed. Tools included in tool_shed_install.xml that have already been installed will not be re-installed. """ +from galaxy.tools import ToolSection from galaxy.util.shed_util import * log = logging.getLogger( __name__ ) diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -99,6 +99,44 @@ self.load_section_tag_set( elem, self.tool_panel, tool_path ) elif elem.tag == 'label': self.load_label_tag_set( elem, self.tool_panel ) + def get_tool( self, tool_id, tool_version=None ): + # Attempt to locate the tool in our in-memory dictionary. + if tool_id in self.tools_by_id: + tool = self.tools_by_id[ tool_id ] + if tool_version and tool.version == tool_version: + return tool + else: + return tool + # Handle the case where the tool was used when the tool was included in the Galaxy distribution, + # but now the tool is contained in an installed tool shed repository. In this case, the original + # tool id can be mapped to the new tool id, which is the tool's guid in the tool shed repository. + # This scenarios can occur in workflows and in a history item when the rerun icon is clicked. + # The weakness here is that workflows currently handle only tool ids and not versions. + tool_id_guid_map = self.__get_tool_id_guid_map( tool_id, tool_version=tool_version ) + if tool_id_guid_map: + guid = tool_id_guid_map.guid + if guid in self.tools_by_id: + return self.tools_by_id[ guid ] + # Handle the case where a proprietary tool was initially developed and hosted in a local Galaxy + # instance, but the developer later uploaded the tool to a Galaxy tool shed, removed the original + # tool from the local Galaxy instance and installed the tool's repository from the tool shed. + for k, tool in self.tools_by_id.items(): + if tool_id == tool.old_id: + if tool_version and tool.version == tool_version: + return tool + else: + return tool + return None + def __get_tool_id_guid_map( self, tool_id, tool_version=None ): + if tool_version: + return self.sa_session.query( self.app.model.ToolIdGuidMap ) \ + .filter( and_( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id, + self.app.model.ToolIdGuidMap.table.c.tool_version == tool_version ) ) \ + .first() + else: + return self.sa_session.query( self.app.model.ToolIdGuidMap ) \ + .filter( self.app.model.ToolIdGuidMap.table.c.tool_id == tool_id ) \ + .first() def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): return self.sa_session.query( self.app.model.ToolShedRepository ) \ .filter( and_( self.app.model.ToolShedRepository.table.c.tool_shed == tool_shed, @@ -193,7 +231,7 @@ self.tools_by_id[ tool.id ] = tool key = 'tool_' + tool.id panel_dict[ key ] = tool - log.debug( "Loaded tool: %s %s" % ( tool.id, tool.version ) ) + log.debug( "Loaded tool id: %s, version: %s." % ( tool.id, tool.version ) ) except: log.exception( "error reading tool from path: %s" % path ) def load_workflow_tag_set( self, elem, panel_dict ): diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/visualization/tracks/visual_analytics.py --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ b/lib/galaxy/visualization/tracks/visual_analytics.py @@ -44,7 +44,7 @@ # assert job is not None, 'Requested job has not been loaded.' if not job: return {} - tool = trans.app.toolbox.tools_by_id.get( job.tool_id, None ) + tool = trans.app.toolbox.get_tool( job.tool_id ) # TODO: could use this assertion to provide more information. # assert tool is not None, 'Requested tool has not been loaded.' if not tool: diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/api/workflows.py --- a/lib/galaxy/web/api/workflows.py +++ b/lib/galaxy/web/api/workflows.py @@ -171,7 +171,7 @@ for i, step in enumerate( workflow.steps ): job = None if step.type == 'tool' or step.type is None: - tool = self.app.toolbox.tools_by_id[ step.tool_id ] + tool = self.app.toolbox.get_tool( step.tool_id ) def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): if prefixed_name in step.input_connections_by_name: diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py +++ b/lib/galaxy/web/controllers/async.py @@ -42,7 +42,7 @@ # initialize the tool toolbox = self.get_toolbox() - tool = toolbox.tools_by_id.get(tool_id, '') + tool = toolbox.get_tool( tool_id ) if not tool: return "Tool with id %s not found" % tool_id diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -1116,7 +1116,7 @@ try: # Load the tool toolbox = self.get_toolbox() - tool = toolbox.tools_by_id.get( job.tool_id, None ) + tool = toolbox.get_tool( job.tool_id ) assert tool is not None, 'Requested tool has not been loaded.' params_objects = job.get_param_values( trans.app ) except: diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -613,7 +613,7 @@ #.add_input( "file", "Archived History File", "archive_file", value=None, error=None ) ) # Run job to do import. - history_imp_tool = trans.app.toolbox.tools_by_id[ '__IMPORT_HISTORY__' ] + history_imp_tool = trans.app.toolbox.get_tool( '__IMPORT_HISTORY__' ) incoming = { '__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type } history_imp_tool.execute( trans, incoming=incoming ) return trans.show_message( "Importing history from '%s'. \ @@ -669,7 +669,7 @@ % ( { 'n' : history.name, 's' : url_for( action="export_archive", id=id, qualified=True ) } ) ) # Run job to do export. - history_exp_tool = trans.app.toolbox.tools_by_id[ '__EXPORT_HISTORY__' ] + history_exp_tool = trans.app.toolbox.get_tool( '__EXPORT_HISTORY__' ) params = { 'history_to_export' : history, 'compress' : gzip, diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -965,7 +965,7 @@ def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ): # Set up the traditional tool state/params tool_id = 'upload1' - tool = trans.app.toolbox.tools_by_id[ tool_id ] + tool = trans.app.toolbox.get_tool( tool_id ) state = tool.new_state( trans ) errors = tool.update_state( trans, tool.inputs_by_page[0], state.inputs, kwd ) tool_params = state.inputs diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -39,7 +39,7 @@ filter( self.app.model.Job.user==trans.user ). \ order_by( self.app.model.Job.create_time.desc() ): tool_id = row[0] - a_tool = toolbox.tools_by_id.get( tool_id, None ) + a_tool = toolbox.get_tool( tool_id ) if a_tool and not a_tool.hidden and a_tool not in recent_tools: recent_tools.append( a_tool ) ## TODO: make number of recently used tools a user preference. @@ -78,7 +78,7 @@ def tool_help( self, trans, id ): """Return help page for tool identified by 'id' if available""" toolbox = self.get_toolbox() - tool = toolbox.tools_by_id.get(id, '') + tool = toolbox.get_tool( id ) yield "<html><body>" if not tool: yield "Unknown tool id '%d'" % id @@ -179,7 +179,7 @@ job_hda = job_hda.copied_from_history_dataset_association force_history_refresh = False if job_hda.creating_job_associations: - tool = trans.app.toolbox.tools_by_id.get( job_hda.creating_job_associations[ 0 ].job.tool_id, None ) + tool = trans.app.toolbox.get_tool( job_hda.creating_job_associations[ 0 ].job.tool_id ) if tool: force_history_refresh = tool.force_history_refresh if not job_hda.visible: diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -49,7 +49,7 @@ else: tool_ids = [ tool_id ] for tool_id in tool_ids: - tool = toolbox.tools_by_id.get( tool_id, None ) + tool = toolbox.get_tool( tool_id ) if tool: break # No tool matching the tool id, display an error (shouldn't happen) @@ -112,7 +112,7 @@ try: # Load the tool toolbox = self.get_toolbox() - tool = toolbox.tools_by_id.get( tool_id, None ) + tool = toolbox.get_tool( tool_id ) assert tool is not None, 'Requested tool has not been loaded.' except: #this is expected, so not an exception @@ -202,7 +202,7 @@ else: library_bunch = None return upload_common.new_upload( trans, cntrller, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD ) - tool = self.get_toolbox().tools_by_id.get( tool_id, None ) + tool = self.get_toolbox().get_tool( tool_id ) if not tool: return False # bad tool_id nonfile_params = util.Params( kwd, sanitize=False ) diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -787,7 +787,7 @@ # # Execute tool. # - tool = trans.app.toolbox.tools_by_id.get( tool_id, None ) + tool = trans.app.toolbox.get_tool( tool_id ) if not tool: return messages.NO_TOOL @@ -829,7 +829,7 @@ # have priority. # original_job = get_dataset_job( original_dataset ) - tool = trans.app.toolbox.tools_by_id.get( original_job.tool_id, None ) + tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool: return messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -925,7 +925,7 @@ filter( self.app.model.History.user==trans.user ). \ order_by( self.app.model.Job.create_time.desc() ).limit(1) tool_id = query[0][0] # Get first element in first row of query. - tool = self.get_toolbox().tools_by_id[ tool_id ] + tool = self.get_toolbox().get_tool( tool_id ) # Return tool info. tool_info = { diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1306,16 +1306,7 @@ for job_id in job_ids: assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" job = jobs_by_id[ job_id ] - try: - tool = trans.app.toolbox.tools_by_id[ job.tool_id ] - except KeyError, e: - # Handle the case where the workflow requires a tool not available in the local Galaxy instance. - # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id - # attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if job.tool_id == available_tool.old_id: - tool = available_tool - break + tool = trans.app.toolbox.get_tool( job.tool_id ) param_values = job.get_param_values( trans.app ) associations = cleanup_param_values( tool.inputs, param_values ) # Doing it this way breaks dynamic parameters, backed out temporarily. @@ -1482,16 +1473,7 @@ # Execute module job = None if step.type == 'tool' or step.type is None: - try: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - except KeyError, e: - # Handle the case where the workflow requires a tool not available in the local Galaxy instance. - # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id - # attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if step.tool_id == available_tool.old_id: - tool = available_tool - break + tool = trans.app.toolbox.get_tool( step.tool_id ) input_values = step.state.inputs # Connect up def callback( input, value, prefixed_name, prefixed_label ): diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -476,6 +476,200 @@ message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) status = 'error' return message, status +def reset_all_repository_metadata( trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, id ) + log.debug( "Resetting all metadata on repository: %s" % repository.name ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + if len( repo ) == 1: + message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) + else: + # The list of changeset_revisions refers to repository_metadata records that have been + # created or updated. When the following loop completes, we'll delete all repository_metadata + # records for this repository that do not have a changeset_revision value in this list. + changeset_revisions = [] + ancestor_changeset_revision = None + ancestor_metadata_dict = None + for changeset in repo.changelog: + current_changeset_revision = str( repo.changectx( changeset ) ) + ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) + if current_changeset_revision == repository.tip: + current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) + else: + current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir ) + if current_metadata_dict: + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparsion will be one of: + # 'no metadata' - no metadata for either ancestor or current, so continue from current + # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current + # 'subset' - ancestor metadata is a subset of current metadata, so continue from current + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current + # metadata, so persist ancestor metadata. + comparison = compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) + if comparison in [ 'no metadata', 'equal', 'subset' ]: + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + elif comparison == 'not equal and not subset': + create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) + # Keep track of the changeset_revisions that we've persisted. + changeset_revisions.append( ancestor_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + else: + # We're either at the first change set in the change log or we have just created or updated + # a repository_metadata record. At this point we set the ancestor changeset to the current + # changeset for comparison in the next iteration. + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + if not ctx.children(): + # We're at the end of the change log. + create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict ) + changeset_revisions.append( current_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + elif ancestor_metadata_dict: + # Our current change set has no metadata, but our ancestor change set has metadata, so save it. + create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) + # Keep track of the changeset_revisions that we've persisted. + changeset_revisions.append( ancestor_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + clean_repository_metadata( trans, id, changeset_revisions ) +def clean_repository_metadata( trans, id, changeset_revisions ): + # Delete all repository_metadata reecords associated with the repository + # that have a changeset_revision that is not in changeset_revisions. + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ): + if repository_metadata.changeset_revision not in changeset_revisions: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() +def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + # Update RepositoryMetadata.metadata. + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # Create a new repository_metadata table row. + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() +def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): + # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision + # is an ancestor of current_changeset_revision which is associated with current_metadata_dict. + # + # TODO: a new repository_metadata record will be created only when this method returns the string + # 'not equal and not subset'. However, we're currently also returning the strings 'no metadata', + # 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave things this way + # for the current time in case we discover a use for these additional result strings. + # + # Get information about tools. + if 'tools' in ancestor_metadata_dict: + ancestor_tools = ancestor_metadata_dict[ 'tools' ] + else: + ancestor_tools = [] + if 'tools' in current_metadata_dict: + current_tools = current_metadata_dict[ 'tools' ] + else: + current_tools = [] + ancestor_guids = [] + for tool_dict in ancestor_tools: + ancestor_guids.append( tool_dict[ 'guid' ] ) + ancestor_guids.sort() + current_guids = [] + for tool_dict in current_tools: + current_guids.append( tool_dict[ 'guid' ] ) + current_guids.sort() + # Get information about workflows. + if 'workflows' in ancestor_metadata_dict: + ancestor_workflows = ancestor_metadata_dict[ 'workflows' ] + else: + ancestor_workflows = [] + if 'workflows' in current_metadata_dict: + current_workflows = current_metadata_dict[ 'workflows' ] + else: + current_workflows = [] + # Get information about datatypes. + if 'datatypes' in ancestor_metadata_dict: + ancestor_datatypes = ancestor_metadata_dict[ 'datatypes' ] + else: + ancestor_datatypes = [] + if 'datatypes' in current_metadata_dict: + current_datatypes = current_metadata_dict[ 'datatypes' ] + else: + current_datatypes = [] + # Handle case where no metadata exists for either changeset. + if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: + return 'no metadata' + workflow_comparison = compare_workflows( ancestor_workflows, current_workflows ) + datatype_comparison = compare_datatypes( ancestor_datatypes, current_datatypes ) + # Handle case where all metadata is the same. + if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': + return 'equal' + if workflow_comparison == 'subset' and datatype_comparison == 'subset': + is_subset = True + for guid in ancestor_guids: + if guid not in current_guids: + is_subset = False + break + if is_subset: + return 'subset' + return 'not equal and not subset' +def compare_workflows( ancestor_workflows, current_workflows ): + # Determine if ancestor_workflows is the same as current_workflows + # or if ancestor_workflows is a subset of current_workflows. + if len( ancestor_workflows ) <= len( current_workflows ): + for ancestor_workflow in ancestor_workflows: + # Currently the only way to differentiate workflows is by name. + ancestor_workflow_name = ancestor_workflow[ 'name' ] + num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] ) + found_in_current = False + for current_workflow in current_workflows: + # Assume that if the name and number of steps are euqal, + # then the workflows are the same. Of course, this may + # not be true... + if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_workflows ) == len( current_workflows ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' +def compare_datatypes( ancestor_datatypes, current_datatypes ): + # Determine if ancestor_datatypes is the same as current_datatypes + # or if ancestor_datatypes is a subset of current_datatypes. Each + # datatype dict looks something like: + # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} + if len( ancestor_datatypes ) <= len( current_datatypes ): + for ancestor_datatype in ancestor_datatypes: + # Currently the only way to differentiate datatypes is by name. + ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] + ancestor_datatype_extension = ancestor_datatype[ 'extension' ] + ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ] + found_in_current = False + for current_datatype in current_datatypes: + if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ + current_datatype[ 'extension' ] == ancestor_datatype_extension and \ + current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_datatypes ) == len( current_datatypes ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1247,15 +1247,21 @@ message = "The selected files were deleted from the repository." else: message = 'No changes to repository.' - # Set metadata on the repository tip + # Set metadata on the repository tip. error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) if error_message: + # If there is an error, display it. message = '%s<br/>%s' % ( message, error_message ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, message=message, status=status ) ) + else: + # If no error occurred in setting metadata on the repository tip, reset metadata on all + # changeset revisions for the repository. This will result in a more standardized set of + # valid repository revisions that can be installed. + reset_all_repository_metadata( trans, id, **kwd ) else: message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" @@ -1723,206 +1729,14 @@ status=status ) ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - if len( repo ) == 1: - message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) - else: - # The list of changeset_revisions refers to repository_metadata records that have been - # created or updated. When the following loop completes, we'll delete all repository_metadata - # records for this repository that do not have a changeset_revision value in this list. - changeset_revisions = [] - ancestor_changeset_revision = None - ancestor_metadata_dict = None - for changeset in repo.changelog: - current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) - if current_changeset_revision == repository.tip: - current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) - else: - current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir ) - if current_metadata_dict: - if ancestor_changeset_revision: - # Compare metadata from ancestor and current. The value of comparsion will be one of: - # 'no metadata' - no metadata for either ancestor or current, so continue from current - # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current - # 'subset' - ancestor metadata is a subset of current metadata, so continue from current - # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current - # metadata, so persist ancestor metadata. - comparison = self.__compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) - if comparison in [ 'no metadata', 'equal', 'subset' ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - elif comparison == 'not equal and not subset': - self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) - # Keep track of the changeset_revisions that we've persisted. - changeset_revisions.append( ancestor_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - else: - # We're either at the first change set in the change log or we have just created or updated - # a repository_metadata record. At this point we set the ancestor changeset to the current - # changeset for comparison in the next iteration. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - if not ctx.children(): - # We're at the end of the change log. - self.__create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict ) - changeset_revisions.append( current_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - elif ancestor_metadata_dict: - # Our current change set has no metadata, but our ancestor change set has metadata, so save it. - self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) - # Keep track of the changeset_revisions that we've persisted. - changeset_revisions.append( ancestor_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - self.__clean_repository_metadata( trans, id, changeset_revisions ) - if not message: - message = "Repository metadata has been reset." - status = 'done' + reset_all_repository_metadata( trans, id, **kwd ) + message = "All repository metadata has been reset." + status = 'done' return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=id, message=message, status=status ) ) - def __clean_repository_metadata( self, trans, id, changeset_revisions ): - # Delete all repository_metadata reecords associated with the repository - # that have a changeset_revision that is not in changeset_revisions. - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ): - if repository_metadata.changeset_revision not in changeset_revisions: - trans.sa_session.delete( repository_metadata ) - trans.sa_session.flush() - def __create_or_update_repository_metadata( self, trans, id, repository, changeset_revision, metadata_dict ): - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - # Update RepositoryMetadata.metadata. - repository_metadata.metadata = metadata_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - else: - # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - def __compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): - # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision - # is an ancestor of current_changeset_revision which is associated with current_metadata_dict. - # - # TODO: a new repository_metadata record will be created only when this method returns the string - # 'not equal and not subset'. However, we're currently also returning the strings 'no metadata', - # 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave things this way - # for the current time in case we discover a use for these additional result strings. - # - # Get information about tools. - if 'tools' in ancestor_metadata_dict: - ancestor_tools = ancestor_metadata_dict[ 'tools' ] - else: - ancestor_tools = [] - if 'tools' in current_metadata_dict: - current_tools = current_metadata_dict[ 'tools' ] - else: - current_tools = [] - ancestor_guids = [] - for tool_dict in ancestor_tools: - ancestor_guids.append( tool_dict[ 'guid' ] ) - ancestor_guids.sort() - current_guids = [] - for tool_dict in current_tools: - current_guids.append( tool_dict[ 'guid' ] ) - current_guids.sort() - # Get information about workflows. - if 'workflows' in ancestor_metadata_dict: - ancestor_workflows = ancestor_metadata_dict[ 'workflows' ] - else: - ancestor_workflows = [] - if 'workflows' in current_metadata_dict: - current_workflows = current_metadata_dict[ 'workflows' ] - else: - current_workflows = [] - # Get information about datatypes. - if 'datatypes' in ancestor_metadata_dict: - ancestor_datatypes = ancestor_metadata_dict[ 'datatypes' ] - else: - ancestor_datatypes = [] - if 'datatypes' in current_metadata_dict: - current_datatypes = current_metadata_dict[ 'datatypes' ] - else: - current_datatypes = [] - # Handle case where no metadata exists for either changeset. - if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: - return 'no metadata' - workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows ) - datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes ) - # Handle case where all metadata is the same. - if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': - return 'equal' - if workflow_comparison == 'subset' and datatype_comparison == 'subset': - is_subset = True - for guid in ancestor_guids: - if guid not in current_guids: - is_subset = False - break - if is_subset: - return 'subset' - return 'not equal and not subset' - def __compare_workflows( self, ancestor_workflows, current_workflows ): - # Determine if ancestor_workflows is the same as current_workflows - # or if ancestor_workflows is a subset of current_workflows. - if len( ancestor_workflows ) <= len( current_workflows ): - for ancestor_workflow in ancestor_workflows: - # Currently the only way to differentiate workflows is by name. - ancestor_workflow_name = ancestor_workflow[ 'name' ] - num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] ) - found_in_current = False - for current_workflow in current_workflows: - # Assume that if the name and number of steps are euqal, - # then the workflows are the same. Of course, this may - # not be true... - if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps: - found_in_current = True - break - if not found_in_current: - return 'not equal and not subset' - if len( ancestor_workflows ) == len( current_workflows ): - return 'equal' - else: - return 'subset' - return 'not equal and not subset' - def __compare_datatypes( self, ancestor_datatypes, current_datatypes ): - # Determine if ancestor_datatypes is the same as current_datatypes - # or if ancestor_datatypes is a subset of current_datatypes. Each - # datatype dict looks something like: - # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} - if len( ancestor_datatypes ) <= len( current_datatypes ): - for ancestor_datatype in ancestor_datatypes: - # Currently the only way to differentiate datatypes is by name. - ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] - ancestor_datatype_extension = ancestor_datatype[ 'extension' ] - ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ] - found_in_current = False - for current_datatype in current_datatypes: - if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ - current_datatype[ 'extension' ] == ancestor_datatype_extension and \ - current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype: - found_in_current = True - break - if not found_in_current: - return 'not equal and not subset' - if len( ancestor_datatypes ) == len( current_datatypes ): - return 'equal' - else: - return 'subset' - return 'not equal and not subset' @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -156,15 +156,21 @@ message += " %d files were removed from the repository root." % len( files_to_remove ) else: message = 'No changes to repository.' - # Set metadata on the repository tip + # Set metadata on the repository tip. error_message, status = set_repository_metadata( trans, repository_id, repository.tip, content_alert_str=content_alert_str, **kwd ) if error_message: + # If there is an error, display it. message = '%s<br/>%s' % ( message, error_message ) return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=repository_id, message=message, status=status ) ) + else: + # If no error occurred in setting metadata on the repository tip, reset metadata on all + # changeset revisions for the repository. This will result in a more standardized set of + # valid repository revisions that can be installed. + reset_all_repository_metadata( trans, repository_id, **kwd ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', id=repository_id, @@ -261,7 +267,7 @@ # file is being uploaded by parsing the file and adding new entries # to the in-memory trans.app.tool_data_tables dictionary as well as # appending them to the shed's tool_data_table_conf.xml file on disk. - error, message = handle_sample_tool_data_table_conf_file( trans, filename_in_archive ) + error, message = handle_sample_tool_data_table_conf_file( trans.app, filename_in_archive ) if error: return False, message, files_to_remove, content_alert_str if filename_in_archive.endswith( '.loc.sample' ): diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -166,17 +166,7 @@ def __init__( self, trans, tool_id ): self.trans = trans self.tool_id = tool_id - try: - self.tool = trans.app.toolbox.tools_by_id[ tool_id ] - except KeyError, e: - # Handle the case where the workflow requires a tool not available in the local Galaxy instance. - self.tool = None - # The id value of tools installed from a Galaxy tool shed is a guid, but - # these tool's old_id attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if tool_id == available_tool.old_id: - self.tool = available_tool - break + self.tool = trans.app.toolbox.get_tool( tool_id ) self.post_job_actions = {} self.workflow_outputs = [] self.state = None @@ -206,12 +196,14 @@ tool_id = step.tool_id install_tool_id = None if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id: - # The id value of tools installed from a Galaxy tool shed is a guid, but - # these tool's old_id attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if tool_id == available_tool.old_id: - install_tool_id = available_tool_id - break + # Handle the case where the tool was used when the tool was included in the Galaxy distribution, + # but now the tool is contained in an installed tool shed repository. In this case, the original + # tool id can be mapped to the new tool id, which is the tool's guid in the tool shed repository. + tool_id_guid_map = trans.sa_session.query( trans.model.ToolIdGuidMap ) \ + .filter( trans.model.ToolIdGuidMap.table.c.tool_id == tool_id ) \ + .first() + if tool_id_guid_map: + install_tool_id = tool_id_guid_map.guid if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id: module = Class( trans, tool_id ) module.state = DefaultToolState() diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -48,7 +48,7 @@ Info: </label><div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="info" value="${data.info}" size="40"/> + <textarea name="info" cols="40" rows="2">${data.info | h}</textarea></div><div style="clear: both"></div></div> @@ -58,7 +58,7 @@ Annotation / Notes: </label><div style="float: left; width: 250px; margin-right: 10px;"> - <textarea name="annotation" cols="40" rows="2">${data_annotation}</textarea> + <textarea name="annotation" cols="40" rows="2">${data_annotation | h}</textarea></div><div style="clear: both"></div><div class="toolParamHelp">Add an annotation or notes to a dataset; annotations are available when a history is viewed.</div> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 templates/history/display_structured.mako --- a/templates/history/display_structured.mako +++ b/templates/history/display_structured.mako @@ -98,8 +98,9 @@ <div class="tool toolForm"><% - if job.tool_id in trans.app.toolbox.tools_by_id: - tool_name = trans.app.toolbox.tools_by_id[job.tool_id].name + tool = trans.app.toolbox.get_tool( job.tool_id ) + if tool: + tool_name = tool.name else: tool_name = "Unknown tool with id '%s'" % job.tool_id %> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 templates/workflow/build_from_current_history.mako --- a/templates/workflow/build_from_current_history.mako +++ b/templates/workflow/build_from_current_history.mako @@ -103,7 +103,7 @@ cls += " toolFormDisabled" disabled = True else: - tool = app.toolbox.tools_by_id.get( job.tool_id, None ) + tool = app.toolbox.get_tool( job.tool_id ) if tool: tool_name = tool.name if tool is None or not( tool.is_workflow_compatible ): diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -83,15 +83,7 @@ <tr><td> %if step.type == 'tool' or step.type is None: <% - try: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - except KeyError, e: - # The id value of tools installed from a Galaxy tool shed is a guid, but - # these tool's old_id attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if step.tool_id == available_tool.old_id: - tool = available_tool - break + tool = trans.app.toolbox.get_tool( step.tool_id ) %><div class="toolForm"><div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 templates/workflow/run.mako --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -364,15 +364,7 @@ %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: <% - try: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - except KeyError, e: - # The id value of tools installed from a Galaxy tool shed is a guid, but - # these tool's old_id attribute should contain what we're looking for. - for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): - if step.tool_id == available_tool.old_id: - tool = available_tool - break + tool = trans.app.toolbox.get_tool( step.tool_id ) %><input type="hidden" name="${step.id}|tool_state" value="${step.state.encode( tool, app )}"><div class="toolForm"> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 test-data/tophat_out1j.bed --- a/test-data/tophat_out1j.bed +++ b/test-data/tophat_out1j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 400 JUNC00000001 26 + 180 400 255,0,0 2 70,50 0,170 -test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 test-data/tophat_out2j.bed --- a/test-data/tophat_out2j.bed +++ b/test-data/tophat_out2j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 177 400 JUNC00000001 61 + 177 400 255,0,0 2 73,50 0,173 -test_chromosome 350 550 JUNC00000002 45 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 test-data/tophat_out3j.bed --- a/test-data/tophat_out3j.bed +++ b/test-data/tophat_out3j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 177 400 JUNC00000001 32 + 177 400 255,0,0 2 73,50 0,173 -test_chromosome 350 550 JUNC00000002 26 + 350 550 255,0,0 2 50,50 0,150 +test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 test-data/tophat_out4j.bed --- a/test-data/tophat_out4j.bed +++ b/test-data/tophat_out4j.bed @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 49 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 +test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 +test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -149,7 +149,7 @@ # Push all the toolbox tests to module level G = globals() for i, tool_id in enumerate( toolbox.tools_by_id ): - tool = toolbox.tools_by_id[ tool_id ] + tool = toolbox.get_tool( tool_id ) if tool.tests: # Create a new subclass of ToolTestCase dynamically adding methods # names test_tool_XXX that run each test defined in the tool. diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.4"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.5"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -329,11 +329,12 @@ <when value="advanced"><repeat name="stratifications" title="Stratification"><param name="select_exps" value="" type="text" label="Stratification Expression"> - <sanitizer> - <valid> - <add value="""/> - </valid> - </sanitizer> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer></param><param name="select_name" value="" type="text" label="Name"/></repeat> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -1,9 +1,10 @@ -<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.3"> +<tool id="gatk_variant_filtration" name="Variant Filtration" version="0.0.4"><description>on VCF files</description><requirements><requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py + #from binascii import hexlify --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" @@ -17,12 +18,11 @@ #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if + ' #for $variant_filter in $variant_filters: - --${variant_filter.is_genotype_filter}Expression "${variant_filter.filter_expression}" - --${variant_filter.is_genotype_filter}Name "${variant_filter.filter_name}" + #set $variant_filter = "--%sExpression '%s' --%sName '%s'" % ( str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_expression ), str( $variant_filter.is_genotype_filter ), str( $variant_filter.filter_name ) ) + -o '${ hexlify( $variant_filter ) }' #end for - ' - #if str( $mask_rod_bind_type.mask_rod_bind_type_selector ) == 'set_mask': -d "--mask:${mask_rod_bind_type.mask_rod_name},%(file_type)s" "${mask_rod_bind_type.input_mask_rod}" "${mask_rod_bind_type.input_mask_rod.ext}" "input_mask_${mask_rod_bind_type.mask_rod_name}" @@ -125,7 +125,6 @@ <sanitizer><valid initial="string.printable"><remove value="'"/> - <remove value="""/></valid><mapping initial="none"/></sanitizer> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/new_operations/concat.xml --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -1,4 +1,4 @@ -<tool id="gops_concat_1" name="Concatenate"> +<tool id="gops_concat_1" name="Concatenate" version="1.0.1"><description>two datasets into one dataset</description><command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command><inputs> diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/new_operations/gops_concat.py --- a/tools/new_operations/gops_concat.py +++ b/tools/new_operations/gops_concat.py @@ -43,6 +43,7 @@ chrom_col=chr_col_1, start_col=start_col_1, end_col=end_col_1, + strand_col=strand_col_1, fix_strand=True ) g2 = NiceReaderWrapper( fileinput.FileInput( in_file_2 ), @@ -52,9 +53,6 @@ strand_col=strand_col_2, fix_strand=True ) - if strand_col_1 >= 0: - g1.strand_col = strand_col_1 - out_file = open( out_fname, "w" ) try: diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -210,6 +210,7 @@ tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) + print cmd proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) returncode = proc.wait() tmp_stderr.close() diff -r 7c3c507843740ce7cb766c11559bde58fdcc7916 -r e250efd2a19c0bb214f02f09451b3afb3165e401 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -518,7 +518,7 @@ <test><!-- Tophat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 - tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger + tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -561,7 +561,7 @@ <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters --><test><!-- TopHat commands: - tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger + tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger Replace the + with double-dash Rename the files in tmp_dir appropriately --> @@ -589,13 +589,7 @@ <param name="use_annotations" value="No" /><param name="use_juncs" value="No" /><param name="no_novel_juncs" value="No" /> - <param name="use_search" value="Yes" /> - <param name="min_closure_exon" value="50" /> - <param name="min_closure_intron" value="50" /> - <param name="max_closure_intron" value="5000" /> - <param name="use_search" value="Yes" /> - <param name="min_coverage_intron" value="50" /> - <param name="max_coverage_intron" value="20000" /> + <param name="use_search" value="No" /><param name="microexon_search" value="Yes" /><output name="junctions" file="tophat_out4j.bed" /><output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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