galaxy-commits December 2011

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commit/galaxy-central: jgoecks: Set Cufflinks global model when upper quartile normalization is used.
by Bitbucket 22 Dec '11

22 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/21b645303c02/ changeset: 21b645303c02 user: jgoecks date: 2011-12-22 19:54:33 summary: Set Cufflinks global model when upper quartile normalization is used. affected #: 1 file diff -r d6d62cb3cf7ea7b7a11a5ca4caf4a85c50a31a93 -r 21b645303c0221690a0114b021cd5e706b0c917a tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -137,11 +137,11 @@ returncode = proc.wait() tmp_stderr.close() - # Read standard error to get total map mass. + # Read standard error to get total map/upper quartile mass. total_map_mass = -1 tmp_stderr = open( tmp_name, 'r' ) for line in tmp_stderr: - if line.lower().find( "total map mass") >= 0: + if line.lower().find( "total map mass" ) >= 0 or line.lower().find( "upper quartile" ) >= 0: total_map_mass = float( line.split(":")[1].strip() ) break tmp_stderr.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: when running tools, replace track with group.
by Bitbucket 22 Dec '11

22 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d6d62cb3cf7e/ changeset: d6d62cb3cf7e user: jgoecks date: 2011-12-22 19:11:34 summary: Trackster: when running tools, replace track with group. affected #: 1 file diff -r 83756dd3d868aee6d319f0d1904a1dcdda12b5b9 -r d6d62cb3cf7ea7b7a11a5ca4caf4a85c50a31a93 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -946,6 +946,20 @@ return false; }, /** + * Replace one drawable with another. + */ + replace_drawable: function(old_drawable, new_drawable, update_html) { + var index = this.drawables.indexOf(old_drawable); + if (index !== -1) { + this.drawables[index] = new_drawable; + if (update_html) { + old_drawable.container_div.replaceWith(new_drawable.container_div); + } + return true; + } + return false; + }, + /** * Remove drawable from this collection. */ remove_drawable: function(drawable) { @@ -1002,7 +1016,11 @@ } ].concat(Drawable.prototype.action_icons_def), build_container_div: function() { - return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); + var container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id); + if (this.container) { + this.container.content_div.append(container_div); + } + return container_div; }, build_header_div: function() { var header_div = $("<div/>").addClass("track-header"); @@ -1787,8 +1805,9 @@ // 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. if (current_track.container === view) { - var group = new DrawableGroup(this.name, this.track.view, this.track.container); - current_track.container.add_drawable(group); + // Create new group. + var group = new DrawableGroup(this.name, this.track.view); + current_track.container.replace_drawable(current_track, group, true); // TODO: this is ugly way to move track from one container to another -- make this easier via // a Drawable or DrawableCollection function. current_track.container.remove_drawable(current_track); @@ -1797,6 +1816,7 @@ container = group; } else { + // Use current group. container = current_track.container; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use integer for dummy filter value rather than string because it is easier for client to decode.
by Bitbucket 22 Dec '11

22 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/83756dd3d868/ changeset: 83756dd3d868 user: jgoecks date: 2011-12-22 16:43:17 summary: Trackster: use integer for dummy filter value rather than string because it is easier for client to decode. affected #: 1 file diff -r 356e8b9510a965d09226c450746dfa2ba267a42c -r 83756dd3d868aee6d319f0d1904a1dcdda12b5b9 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -1053,5 +1053,5 @@ payload.append( feature.attributes[col] ) else: # Dummy value. - payload.append( "na" ) + payload.append( 0 ) return payload Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
by Bitbucket 21 Dec '11

21 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/356e8b9510a9/ changeset: 356e8b9510a9 user: jgoecks date: 2011-12-21 23:04:23 summary: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster. affected #: 6 files diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -29,6 +29,7 @@ from cgi import FieldStorage from galaxy.util.hash_util import * from galaxy.util import listify +from galaxy.visualization.tracks.visual_analytics import TracksterConfig log = logging.getLogger( __name__ ) @@ -567,7 +568,11 @@ # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible() # Trackster configuration. - self.trackster_conf = ( root.find( "trackster_conf" ) is not None ) + trackster_conf = root.find( "trackster_conf" ) + if trackster_conf: + self.trackster_conf = TracksterConfig.parse( trackster_conf ) + else: + self.trackster_conf = None def parse_inputs( self, root ): """ diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1549,6 +1549,22 @@ if call_attribute: ref = ref() return ref + +class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): + """ + Hidden parameter that behaves as a DataToolParameter. As with all hidden + parameters, this is a HACK. + """ + def __init__( self, tool, elem ): + DataToolParameter.__init__( self, tool, elem ) + self.value = "None" + + def get_initial_value( self, trans, context ): + return None + + def get_html_field( self, trans=None, value=None, other_values={} ): + return form_builder.HiddenField( self.name, self.value ) + class LibraryDatasetToolParameter( ToolParameter ): """ @@ -1644,6 +1660,7 @@ select = SelectToolParameter, data_column = ColumnListParameter, hidden = HiddenToolParameter, + hidden_data = HiddenDataToolParameter, baseurl = BaseURLToolParameter, file = FileToolParameter, ftpfile = FTPFileToolParameter, diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/visualization/tracks/visual_analytics.py --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ b/lib/galaxy/visualization/tracks/visual_analytics.py @@ -3,6 +3,31 @@ from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter from galaxy.tools.parameters.dynamic_options import DynamicOptions +class TracksterConfig: + """ Trackster configuration encapsulation. """ + + def __init__( self, actions ): + self.actions = actions + + @staticmethod + def parse( root ): + actions = [] + for action_elt in root.findall( "action" ): + actions.append( SetParamAction.parse( action_elt ) ) + return TracksterConfig( actions ) + +class SetParamAction: + """ Set parameter action. """ + + def __init__( self, name, output_name ): + self.name = name + self.output_name = output_name + + @staticmethod + def parse( elt ): + """ Parse action from element. """ + return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + def get_dataset_job( hda ): # Get dataset's job. job = None diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -824,7 +824,7 @@ return to_json_string( msg ) # - # Set tool parameters--except dataset parameters--using combination of + # Set tool parameters--except non-hidden dataset parameters--using combination of # job's previous parameters and incoming parameters. Incoming parameters # have priority. # @@ -872,15 +872,10 @@ else: target_history = trans.get_history( create=True ) hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history ) - - # - # 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. + Set new parameter value in a tool's parameter dictionary. """ # Recursive function to set param value. @@ -913,8 +908,30 @@ group_index = int( group[ index + 1: ] ) return set_value( param_dict, group_name, group_index, param_name, param_value ) - + + # Set parameters based tool's trackster config. + params_set = {} + for action in tool.trackster_conf.actions: + success = False + for joda in original_job.output_datasets: + if joda.name == action.output_name: + set_param_value( tool_params, action.name, joda.dataset ) + params_set[ action.name ] = True + success = True + break + + if not success: + return messages.ERROR + + # + # Set input datasets for tool. If running on region, extract and use subset + # when possible. + # for jida in original_job.input_datasets: + # If param set previously by config actions, do nothing. + if jida.name in params_set: + continue + input_dataset = jida.dataset if input_dataset is None: #optional dataset and dataset wasn't selected tool_params[ jida.name ] = None diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -1,6 +1,8 @@ #!/usr/bin/env python import optparse, os, shutil, subprocess, sys, tempfile +from galaxy import eggs +from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -51,6 +53,9 @@ parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) + # Global model. + parser.add_option( '', '--global_model', dest='global_model_file', help='Global model used for computing on local data' ) + (options, args) = parser.parse_args() # output version # of tool @@ -122,7 +127,9 @@ # Add input files. cmd += " " + options.input + # # Run command. + # try: tmp_name = tempfile.NamedTemporaryFile( dir="." ).name tmp_stderr = open( tmp_name, 'wb' ) @@ -130,7 +137,60 @@ returncode = proc.wait() tmp_stderr.close() - # Get stderr, allowing for case where it's very large. + # Read standard error to get total map mass. + total_map_mass = -1 + tmp_stderr = open( tmp_name, 'r' ) + for line in tmp_stderr: + if line.lower().find( "total map mass") >= 0: + total_map_mass = float( line.split(":")[1].strip() ) + break + tmp_stderr.close() + + # + # If there's a global model provided, use model's total map mass + # to adjust FPKM + confidence intervals. + # + if options.global_model_file: + # Global model is simply total map mass from original run. + global_model_file = open( options.global_model_file, 'r' ) + global_model_total_map_mass = float( global_model_file.readline() ) + global_model_file.close() + + # Ratio of global model's total map mass to original run's map mass is + # factor used to adjust FPKM. + fpkm_map_mass_ratio = total_map_mass / global_model_total_map_mass + + # Update FPKM values in transcripts.gtf file. + transcripts_file = open( "transcripts.gtf", 'r' ) + tmp_transcripts = tempfile.NamedTemporaryFile( dir="." ).name + new_transcripts_file = open( tmp_transcripts, 'w' ) + for line in transcripts_file: + fields = line.split( '\t' ) + attrs = parse_gff_attributes( fields[8] ) + attrs[ "FPKM" ] = str( float( attrs[ "FPKM" ] ) * fpkm_map_mass_ratio ) + attrs[ "conf_lo" ] = str( float( attrs[ "conf_lo" ] ) * fpkm_map_mass_ratio ) + attrs[ "conf_hi" ] = str( float( attrs[ "conf_hi" ] ) * fpkm_map_mass_ratio ) + fields[8] = gff_attributes_to_str( attrs, "GTF" ) + new_transcripts_file.write( "%s\n" % '\t'.join( fields ) ) + transcripts_file.close() + new_transcripts_file.close() + shutil.copyfile( tmp_transcripts, "transcripts.gtf" ) + + # TODO: update expression files as well. + + # Set outputs. Transcript and gene expression handled by wrapper directives. + shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file ) + if total_map_mass > -1: + f = open( "global_model.txt", 'w' ) + f.write( "%f\n" % total_map_mass ) + f.close() + + # Error checking. + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise e + # Read stderr so that it can be reported: tmp_stderr = open( tmp_name, 'rb' ) stderr = '' buffsize = 1048576 @@ -142,14 +202,7 @@ except OverflowError: pass tmp_stderr.close() - - # Copy outputs. - shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file ) - # Error checking. - if returncode != 0: - raise Exception, stderr - except Exception, e: stop_err( 'Error running cufflinks. ' + str( e ) ) if __name__=="__main__": __main__() diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -43,6 +43,11 @@ --dbkey=${input.metadata.dbkey} --index_dir=${GALAXY_DATA_INDEX_DIR} #end if + + ## Include global model if available. + #if $global_model: + --global_model=$global_model + #end if </command><inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> @@ -97,15 +102,20 @@ <param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/></when></conditional> + <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs><outputs><data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/><data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> + <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/></outputs> - <trackster_conf/> + <trackster_conf> + <action type="set_param" name="global_model" output_name="total_map_mass"/> + </trackster_conf> + <tests><!-- Simple test that uses test data included with cufflinks. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: clements: Updated "Example" images shown at the bottom of many
by Bitbucket 21 Dec '11

21 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/38fcdb8f0e63/ changeset: 38fcdb8f0e63 user: clements date: 2011-12-19 11:44:31 summary: Updated "Example" images shown at the bottom of many "Operate on Genomic Invervals" tool pages. Old onew were looking dated. New ones look, well, newer, and cover more cases. affected #: 20 files diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_baseCoverage.gif Binary file static/operation_icons/gops_baseCoverage.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterFind.gif Binary file static/operation_icons/gops_clusterFind.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterMerge.gif Binary file static/operation_icons/gops_clusterMerge.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_complement.gif Binary file static/operation_icons/gops_complement.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_concatenate.gif Binary file static/operation_icons/gops_concatenate.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingIntervals.gif Binary file static/operation_icons/gops_intersectOverlappingIntervals.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingPieces.gif Binary file static/operation_icons/gops_intersectOverlappingPieces.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinFullOuter.gif Binary file static/operation_icons/gops_joinFullOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinInner.gif Binary file static/operation_icons/gops_joinInner.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinLeftOuter.gif Binary file static/operation_icons/gops_joinLeftOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRecordsList.gif Binary file static/operation_icons/gops_joinRecordsList.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRightOuter.gif Binary file static/operation_icons/gops_joinRightOuter.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_merge.gif Binary file static/operation_icons/gops_merge.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingIntervals.gif Binary file static/operation_icons/gops_subtractOverlappingIntervals.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingPieces.gif Binary file static/operation_icons/gops_subtractOverlappingPieces.gif has changed diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/basecoverage.xml --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -36,6 +36,10 @@ .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations +**Example** + +.. image:: ./static/operation_icons/gops_baseCoverage.gif + </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/cluster.xml --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -82,9 +82,15 @@ ----- -**Example** +**Examples** -.. image:: ./static/operation_icons/gops_cluster.gif +Find Clusters: + +.. image:: ./static/operation_icons/gops_clusterFind.gif + +Merge Clusters: + +.. image:: ./static/operation_icons/gops_clusterMerge.gif </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -129,9 +129,15 @@ ----- -**Example** +**Examples** -.. image:: ./static/operation_icons/gops_intersect.gif +Overlapping Intervals: + +.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif + +Overlapping Pieces of Intervals: + +.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/join.xml --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -92,48 +92,26 @@ ----- -**Example** +**Examples** -If **First dataset** is:: +.. image:: ./static/operation_icons/gops_joinRecordsList.gif - chr1 10 100 Query1.1 - chr1 500 1000 Query1.2 - chr1 1100 1250 Query1.3 +Only records that are joined (inner join): -and **Second dataset** is:: +.. image:: ./static/operation_icons/gops_joinInner.gif - chr1 20 80 Query2.1 - chr1 2000 2204 Query2.2 - chr1 2500 3000 Query2.3 +All records of first dataset: +.. image:: ./static/operation_icons/gops_joinLeftOuter.gif -The four return options will generate: +All records of second dataset: +.. image:: ./static/operation_icons/gops_joinRightOuter.gif -- **Return only records that are joined**:: +All records of both datasets: - chr1 10 100 Query1.1 chr1 20 80 Query2.1 +.. image:: ./static/operation_icons/gops_joinFullOuter.gif -- **Return all records of first dataset**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - chr1 500 1000 Query1.2 . . . . - chr1 1100 1250 Query1.3 . . . . - -- **Return all records of second dataset**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - . . . . chr1 2000 2204 Query2.2 - . . . . chr1 2500 3000 Query2.3 - -- **Return all records of both datasets**:: - - chr1 10 100 Query1.1 chr1 20 80 Query2.1 - chr1 500 1000 Query1.2 . . . . - chr1 1100 1250 Query1.3 . . . . - . . . . chr1 2000 2204 Query2.2 - . . . . chr1 2500 3000 Query2.3 - </help> -</tool> \ No newline at end of file +</tool> diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/subtract.xml --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -112,7 +112,13 @@ **Example** -.. image:: ./static/operation_icons/gops_subtract.gif +Intervals with no overlap: + +.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif + +Non-overlapping pieces of intervals: + +.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add UCSC VCF external display application.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb5e05256c29/ changeset: bb5e05256c29 user: dan date: 2011-12-20 21:40:07 summary: Add UCSC VCF external display application. affected #: 2 files diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -162,6 +162,7 @@ <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="ucsc/vcf.xml" /><display file="igv/vcf.xml" /></datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/> diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d display_applications/ucsc/vcf.xml --- /dev/null +++ b/display_applications/ucsc/vcf.xml @@ -0,0 +1,17 @@ +<display id="ucsc_vcf" version="1.0.0" name="display at UCSC"> +  + <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0"> +  + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="ucsc_link" value="1"/> + <dynamic_param name="builds" value="2" split="True" separator="," /> +  + <filter>${site_id in $APP.config.ucsc_display_sites}</filter> + <filter>${dataset.dbkey in $builds}</filter> +  + <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&hgt.customText=${qp($track.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="track" viewable="True">track type="vcfTabix" name="${bgzip_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bgzip_file.url}" db="${bgzip_file.dbkey}"</param> + </dynamic_links> +</display> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Don't allow repository names to be changed if the repository has been cloned at least 1 time.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f22a8a7bd077/ changeset: f22a8a7bd077 user: greg date: 2011-12-20 20:31:13 summary: Don't allow repository names to be changed if the repository has been cloned at least 1 time. affected #: 1 file diff -r 8458fa9dd5590e0890effaf04c50ba19013a280c -r f22a8a7bd077a118bcfa71430f345ff46873757f templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -139,7 +139,14 @@ %endif <div class="form-row"><label>Name:</label> - <input name="repo_name" type="textfield" value="${repo_name}" size="40"/> + %if repository.times_downloaded > 0: + ${repo_name} + %else: + <input name="repo_name" type="textfield" value="${repo_name}" size="40"/> + %endif + <div class="toolParamHelp" style="clear: both;"> + Repository names cannot be changed if the repository has been cloned. + </div><div style="clear: both"></div></div><div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8458fa9dd559/ changeset: 8458fa9dd559 user: greg date: 2011-12-20 20:15:39 summary: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed. affected #: 1 file diff -r 0497ba5576facae84f7b9a44092d0f67a61788ef -r 8458fa9dd5590e0890effaf04c50ba19013a280c tool_shed_install.xml.sample --- a/tool_shed_install.xml.sample +++ b/tool_shed_install.xml.sample @@ -1,114 +1,116 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"> +  + <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><section name="EMBOSS" id="EMBOSSLite"> - <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="PlaceHereWhenKnown"> - <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" /> - <tool file="emboss_5/emboss_backtranseq.xml" id="EMBOSS: backtranseq2" version="5.0.0" /> - <tool file="emboss_5/emboss_banana.xml" id="EMBOSS: banana3" version="5.0.0" /> - <tool file="emboss_5/emboss_biosed.xml" id="EMBOSS: biosed4" version="5.0.0" /> - <tool file="emboss_5/emboss_btwisted.xml" id="EMBOSS: btwisted5" version="5.0.0" /> - <tool file="emboss_5/emboss_cai_custom.xml" id="EMBOSS: cai_custom6" version="5.0.0" /> - <tool file="emboss_5/emboss_cai.xml" id="EMBOSS: cai6" version="5.0.0" /> - <tool file="emboss_5/emboss_chaos.xml" id="EMBOSS: chaos7" version="5.0.0" /> - <tool file="emboss_5/emboss_charge.xml" id="EMBOSS: charge8" version="5.0.0" /> - <tool file="emboss_5/emboss_checktrans.xml" id="EMBOSS: checktrans9" version="5.0.0" /> - <tool file="emboss_5/emboss_chips.xml" id="EMBOSS: chips10" version="5.0.0" /> - <tool file="emboss_5/emboss_cirdna.xml" id="EMBOSS: cirdna11" version="5.0.0" /> - <tool file="emboss_5/emboss_codcmp.xml" id="EMBOSS: codcmp12" version="5.0.0" /> - <tool file="emboss_5/emboss_coderet.xml" id="EMBOSS: coderet13" version="5.0.0" /> - <tool file="emboss_5/emboss_compseq.xml" id="EMBOSS: compseq14" version="5.0.0" /> - <tool file="emboss_5/emboss_cpgplot.xml" id="EMBOSS: cpgplot15" version="5.0.0" /> - <tool file="emboss_5/emboss_cpgreport.xml" id="EMBOSS: cpgreport16" version="5.0.0" /> - <tool file="emboss_5/emboss_cusp.xml" id="EMBOSS: cusp17" version="5.0.0" /> - <tool file="emboss_5/emboss_cutseq.xml" id="EMBOSS: cutseq18" version="5.0.0" /> - <tool file="emboss_5/emboss_dan.xml" id="EMBOSS: dan19" version="5.0.0" /> - <tool file="emboss_5/emboss_degapseq.xml" id="EMBOSS: degapseq20" version="5.0.0" /> - <tool file="emboss_5/emboss_descseq.xml" id="EMBOSS: descseq21" version="5.0.0" /> - <tool file="emboss_5/emboss_diffseq.xml" id="EMBOSS: diffseq22" version="5.0.0" /> - <tool file="emboss_5/emboss_digest.xml" id="EMBOSS: digest23" version="5.0.0" /> - <tool file="emboss_5/emboss_dotmatcher.xml" id="EMBOSS: dotmatcher24" version="5.0.0" /> - <tool file="emboss_5/emboss_dotpath.xml" id="EMBOSS: dotpath25" version="5.0.0" /> - <tool file="emboss_5/emboss_dottup.xml" id="EMBOSS: dottup26" version="5.0.0" /> - <tool file="emboss_5/emboss_dreg.xml" id="EMBOSS: dreg27" version="5.0.0" /> - <tool file="emboss_5/emboss_einverted.xml" id="EMBOSS: einverted28" version="5.0.0" /> - <tool file="emboss_5/emboss_epestfind.xml" id="EMBOSS: epestfind29" version="5.0.0" /> - <tool file="emboss_5/emboss_equicktandem.xml" id="EMBOSS: equicktandem31" version="5.0.0" /> - <tool file="emboss_5/emboss_est2genome.xml" id="EMBOSS: est2genome32" version="5.0.0" /> - <tool file="emboss_5/emboss_etandem.xml" id="EMBOSS: etandem33" version="5.0.0" /> - <tool file="emboss_5/emboss_extractfeat.xml" id="EMBOSS: extractfeat34" version="5.0.0" /> - <tool file="emboss_5/emboss_extractseq.xml" id="EMBOSS: extractseq35" version="5.0.0" /> - <tool file="emboss_5/emboss_freak.xml" id="EMBOSS: freak36" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzznuc.xml" id="EMBOSS: fuzznuc37" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzzpro.xml" id="EMBOSS: fuzzpro38" version="5.0.0" /> - <tool file="emboss_5/emboss_fuzztran.xml" id="EMBOSS: fuzztran39" version="5.0.0" /> - <tool file="emboss_5/emboss_garnier.xml" id="EMBOSS: garnier40" version="5.0.0" /> - <tool file="emboss_5/emboss_geecee.xml" id="EMBOSS: geecee41" version="5.0.0" /> - <tool file="emboss_5/emboss_getorf.xml" id="EMBOSS: getorf42" version="5.0.0" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" id="EMBOSS: helixturnhelix43" version="5.0.0" /> - <tool file="emboss_5/emboss_hmoment.xml" id="EMBOSS: hmoment44" version="5.0.0" /> - <tool file="emboss_5/emboss_iep.xml" id="EMBOSS: iep45" version="5.0.0" /> - <tool file="emboss_5/emboss_infoseq.xml" id="EMBOSS: infoseq46" version="5.0.0" /> - <tool file="emboss_5/emboss_isochore.xml" id="EMBOSS: isochore47" version="5.0.0" /> - <tool file="emboss_5/emboss_lindna.xml" id="EMBOSS: lindna48" version="5.0.0" /> - <tool file="emboss_5/emboss_marscan.xml" id="EMBOSS: marscan49" version="5.0.0" /> - <tool file="emboss_5/emboss_maskfeat.xml" id="EMBOSS: maskfeat50" version="5.0.0" /> - <tool file="emboss_5/emboss_maskseq.xml" id="EMBOSS: maskseq51" version="5.0.0" /> - <tool file="emboss_5/emboss_matcher.xml" id="EMBOSS: matcher52" version="5.0.0" /> - <tool file="emboss_5/emboss_megamerger.xml" id="EMBOSS: megamerger53" version="5.0.0" /> - <tool file="emboss_5/emboss_merger.xml" id="EMBOSS: merger54" version="5.0.0" /> - <tool file="emboss_5/emboss_msbar.xml" id="EMBOSS: msbar55" version="5.0.0" /> - <tool file="emboss_5/emboss_needle.xml" id="EMBOSS: needle56" version="5.0.0" /> - <tool file="emboss_5/emboss_newcpgreport.xml" id="EMBOSS: newcpgreport57" version="5.0.0" /> - <tool file="emboss_5/emboss_newcpgseek.xml" id="EMBOSS: newcpgseek58" version="5.0.0" /> - <tool file="emboss_5/emboss_newseq.xml" id="EMBOSS: newseq59" version="5.0.0" /> - <tool file="emboss_5/emboss_noreturn.xml" id="EMBOSS: noreturn60" version="5.0.0" /> - <tool file="emboss_5/emboss_notseq.xml" id="EMBOSS: notseq61" version="5.0.0" /> - <tool file="emboss_5/emboss_nthseq.xml" id="EMBOSS: nthseq62" version="5.0.0" /> - <tool file="emboss_5/emboss_octanol.xml" id="EMBOSS: octanol63" version="5.0.0" /> - <tool file="emboss_5/emboss_oddcomp.xml" id="EMBOSS: oddcomp64" version="5.0.0" /> - <tool file="emboss_5/emboss_palindrome.xml" id="EMBOSS: palindrome65" version="5.0.0" /> - <tool file="emboss_5/emboss_pasteseq.xml" id="EMBOSS: pasteseq66" version="5.0.0" /> - <tool file="emboss_5/emboss_patmatdb.xml" id="EMBOSS: patmatdb67" version="5.0.0" /> - <tool file="emboss_5/emboss_pepcoil.xml" id="EMBOSS: pepcoil68" version="5.0.0" /> - <tool file="emboss_5/emboss_pepinfo.xml" id="EMBOSS: pepinfo69" version="5.0.0" /> - <tool file="emboss_5/emboss_pepnet.xml" id="EMBOSS: pepnet70" version="5.0.0" /> - <tool file="emboss_5/emboss_pepstats.xml" id="EMBOSS: pepstats71" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwheel.xml" id="EMBOSS: pepwheel72" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwindow.xml" id="EMBOSS: pepwindow73" version="5.0.0" /> - <tool file="emboss_5/emboss_pepwindowall.xml" id="EMBOSS: pepwindowall74" version="5.0.0" /> - <tool file="emboss_5/emboss_plotcon.xml" id="EMBOSS: plotcon75" version="5.0.0" /> - <tool file="emboss_5/emboss_plotorf.xml" id="EMBOSS: plotorf76" version="5.0.0" /> - <tool file="emboss_5/emboss_polydot.xml" id="EMBOSS: polydot77" version="5.0.0" /> - <tool file="emboss_5/emboss_preg.xml" id="EMBOSS: preg78" version="5.0.0" /> - <tool file="emboss_5/emboss_prettyplot.xml" id="EMBOSS: prettyplot79" version="5.0.0" /> - <tool file="emboss_5/emboss_prettyseq.xml" id="EMBOSS: prettyseq80" version="5.0.0" /> - <tool file="emboss_5/emboss_primersearch.xml" id="EMBOSS: primersearch81" version="5.0.0" /> - <tool file="emboss_5/emboss_revseq.xml" id="EMBOSS: revseq82" version="5.0.0" /> - <tool file="emboss_5/emboss_seqmatchall.xml" id="EMBOSS: seqmatchall83" version="5.0.0" /> - <tool file="emboss_5/emboss_seqret.xml" id="EMBOSS: seqret84" version="5.0.0" /> - <tool file="emboss_5/emboss_showfeat.xml" id="EMBOSS: showfeat85" version="5.0.0" /> - <tool file="emboss_5/emboss_shuffleseq.xml" id="EMBOSS: shuffleseq87" version="5.0.0" /> - <tool file="emboss_5/emboss_sigcleave.xml" id="EMBOSS: sigcleave88" version="5.0.0" /> - <tool file="emboss_5/emboss_sirna.xml" id="EMBOSS: sirna89" version="5.0.0" /> - <tool file="emboss_5/emboss_sixpack.xml" id="EMBOSS: sixpack90" version="5.0.0" /> - <tool file="emboss_5/emboss_skipseq.xml" id="EMBOSS: skipseq91" version="5.0.0" /> - <tool file="emboss_5/emboss_splitter.xml" id="EMBOSS: splitter92" version="5.0.0" /> - <tool file="emboss_5/emboss_supermatcher.xml" id="EMBOSS: supermatcher95" version="5.0.0" /> - <tool file="emboss_5/emboss_syco.xml" id="EMBOSS: syco96" version="5.0.0" /> - <tool file="emboss_5/emboss_tcode.xml" id="EMBOSS: tcode97" version="5.0.0" /> - <tool file="emboss_5/emboss_textsearch.xml" id="EMBOSS: textsearch98" version="5.0.0" /> - <tool file="emboss_5/emboss_tmap.xml" id="EMBOSS: tmap99" version="5.0.0" /> - <tool file="emboss_5/emboss_tranalign.xml" id="EMBOSS: tranalign100" version="5.0.0" /> - <tool file="emboss_5/emboss_transeq.xml" id="EMBOSS: transeq101" version="5.0.0" /> - <tool file="emboss_5/emboss_trimest.xml" id="EMBOSS: trimest102" version="5.0.0" /> - <tool file="emboss_5/emboss_trimseq.xml" id="EMBOSS: trimseq103" version="5.0.0" /> - <tool file="emboss_5/emboss_twofeat.xml" id="EMBOSS: twofeat104" version="5.0.0" /> - <tool file="emboss_5/emboss_union.xml" id="EMBOSS: union105" version="5.0.0" /> - <tool file="emboss_5/emboss_vectorstrip.xml" id="EMBOSS: vectorstrip106" version="5.0.0" /> - <tool file="emboss_5/emboss_water.xml" id="EMBOSS: water107" version="5.0.0" /> - <tool file="emboss_5/emboss_wobble.xml" id="EMBOSS: wobble108" version="5.0.0" /> - <tool file="emboss_5/emboss_wordcount.xml" id="EMBOSS: wordcount109" version="5.0.0" /> - <tool file="emboss_5/emboss_wordmatch.xml" id="EMBOSS: wordmatch110" version="5.0.0" /> + <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b"> + <tool id="EMBOSS: antigenic1" version="5.0.0" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" /> + <tool id="EMBOSS: banana3" version="5.0.0" /> + <tool id="EMBOSS: biosed4" version="5.0.0" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" /> + <tool id="EMBOSS: cai6" version="5.0.0" /> + <tool id="EMBOSS: chaos7" version="5.0.0" /> + <tool id="EMBOSS: charge8" version="5.0.0" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" /> + <tool id="EMBOSS: chips10" version="5.0.0" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" /> + <tool id="EMBOSS: coderet13" version="5.0.0" /> + <tool id="EMBOSS: compseq14" version="5.0.0" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" /> + <tool id="EMBOSS: cusp17" version="5.0.0" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" /> + <tool id="EMBOSS: dan19" version="5.0.0" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" /> + <tool id="EMBOSS: descseq21" version="5.0.0" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" /> + <tool id="EMBOSS: digest23" version="5.0.0" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" /> + <tool id="EMBOSS: dottup26" version="5.0.0" /> + <tool id="EMBOSS: dreg27" version="5.0.0" /> + <tool id="EMBOSS: einverted28" version="5.0.0" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" /> + <tool id="EMBOSS: etandem33" version="5.0.0" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" /> + <tool id="EMBOSS: freak36" version="5.0.0" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" /> + <tool id="EMBOSS: garnier40" version="5.0.0" /> + <tool id="EMBOSS: geecee41" version="5.0.0" /> + <tool id="EMBOSS: getorf42" version="5.0.0" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" /> + <tool id="EMBOSS: iep45" version="5.0.0" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" /> + <tool id="EMBOSS: isochore47" version="5.0.0" /> + <tool id="EMBOSS: lindna48" version="5.0.0" /> + <tool id="EMBOSS: marscan49" version="5.0.0" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" /> + <tool id="EMBOSS: matcher52" version="5.0.0" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" /> + <tool id="EMBOSS: merger54" version="5.0.0" /> + <tool id="EMBOSS: msbar55" version="5.0.0" /> + <tool id="EMBOSS: needle56" version="5.0.0" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" /> + <tool id="EMBOSS: newseq59" version="5.0.0" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" /> + <tool id="EMBOSS: notseq61" version="5.0.0" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" /> + <tool id="EMBOSS: octanol63" version="5.0.0" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" /> + <tool id="EMBOSS: polydot77" version="5.0.0" /> + <tool id="EMBOSS: preg78" version="5.0.0" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" /> + <tool id="EMBOSS: revseq82" version="5.0.0" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" /> + <tool id="EMBOSS: seqret84" version="5.0.0" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" /> + <tool id="EMBOSS: sirna89" version="5.0.0" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" /> + <tool id="EMBOSS: splitter92" version="5.0.0" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" /> + <tool id="EMBOSS: syco96" version="5.0.0" /> + <tool id="EMBOSS: tcode97" version="5.0.0" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" /> + <tool id="EMBOSS: tmap99" version="5.0.0" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" /> + <tool id="EMBOSS: transeq101" version="5.0.0" /> + <tool id="EMBOSS: trimest102" version="5.0.0" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" /> + <tool id="EMBOSS: union105" version="5.0.0" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" /> + <tool id="EMBOSS: water107" version="5.0.0" /> + <tool id="EMBOSS: wobble108" version="5.0.0" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" /></repository></section></toolshed> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Ensure that the integrated datatypes registry configs exist when needed.
by Bitbucket 20 Dec '11

20 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0497ba5576fa/ changeset: 0497ba5576fa user: greg date: 2011-12-20 15:38:15 summary: Ensure that the integrated datatypes registry configs exist when needed. affected #: 5 files diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -126,7 +126,7 @@ try: # If the datatypes registry was persisted, attempt to # remove the temporary file in which it was written. - if self.datatypes_registry.xml_filename is not None: - os.unlink( self.datatypes_registry.xml_filename ) + if self.datatypes_registry.integrated_datatypes_configs is not None: + os.unlink( self.datatypes_registry.integrated_datatypes_configs ) except: pass diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -434,6 +434,12 @@ if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype rval[ 'auto' ] = rval[ 'txt' ] return rval + @property + def integrated_datatypes_configs( self ): + if self.xml_filename and os.path.isfile( self.xml_filename ): + return self.xml_filename + self.to_xml_file() + return self.xml_filename def to_xml_file( self ): if self.xml_filename is not None: # If persisted previously, attempt to remove diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -868,7 +868,7 @@ if config_root is None: config_root = self.app.config.root if datatypes_config is None: - datatypes_config = self.app.datatypes_registry.xml_filename + datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], self.sa_session, exec_dir = exec_dir, diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1674,7 +1674,7 @@ # For the upload tool, we need to know the root directory and the # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) - param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename + param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs # Return the dictionary of parameters return param_dict diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -51,7 +51,7 @@ dataset_files_path = trans.app.model.Dataset.file_path, output_fnames = None, config_root = None, - datatypes_config = trans.app.datatypes_registry.xml_filename, + datatypes_config = trans.app.datatypes_registry.integrated_datatypes_configs, job_metadata = None, kwds = { 'overwrite' : overwrite } ) incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Clean up implementation in 303741fda0ec
by Bitbucket 19 Dec '11

19 Dec '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/166ea1ba55cb/ changeset: 166ea1ba55cb user: jgoecks date: 2011-12-19 21:00:53 summary: Clean up implementation in 303741fda0ec affected #: 1 file diff -r 303741fda0ec4ce0fc7b42a0334a6c84f44c7a1f -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -678,7 +678,7 @@ output.count = int( data_elem.get("count", 1) ) output.filters = data_elem.findall( 'filter' ) output.from_work_dir = data_elem.get("from_work_dir", None) - output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ] + output.hidden = util.string_as_bool( data_elem.get("hidden", "") ) output.tool = self output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) ) self.outputs[ output.name ] = output Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits December 2011