galaxy-commits September 2010

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galaxy-dist commit 4ee5fca864a4: lims: find samples
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283367408 14400 # Node ID 4ee5fca864a44b2bf7e7efac7a97f564961df3f2 # Parent f41f4ace420a58e7316fbeddacd301ff6d5dfaf1 lims: find samples - the search settings are saved after the search - search now case insensitive and wildcard support added - masthead problem fixed when showing find samples page in user mode --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -54,47 +54,60 @@ <div class="toolFormBody"><form name="find_request" id="find_request" action="${h.url_for( controller='requests_common', action='find', cntrller=cntrller)}" method="post" ><div class="form-row"> - <label>Find in sequencing requests in state:</label> - <select name="request_state"> - <option value="In Progress" selected>In-Progress</option> - <option value="Complete">Complete</option> - <option value="Both">Both</option> - </select> + <label>Find sample(s) using:</label> + ${search_type.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Select a sample attribute to search through all the samples.<br/> + To search for a sample with a dataset name, select the dataset + option above. This will return all the sample(s) which has a + dataset with the given name associated with it. To search for + all samples created on a certain date select the 'date created' + option above. Enter date in 'YYYY-MM-DD' format. + </div></div><div class="form-row"> - <label>Find by sample:</label> - <select name="search_type"> - <option value="name" selected>name</option> - <option value="bar_code">barcode</option> - </select> + <label>Filter sequencing requests in state:</label> + ${request_states.get_html()} + <div class="toolParamHelp" style="clear: both;"> + This will filter the search results to show only those sample(s) <br/> + whose parent sequencing request is in the selected state. + </div></div><div class="form-row"> - <input type="text" name="search_string" size="40" value=""> - <input type="submit" name="go_button" value="Go"/> + ${search_box.get_html()} + <input type="submit" name="go_button" value="Find"/> + <div class="toolParamHelp" style="clear: both;"> + Wildcard search (%) can be used as placeholder for any sequence of characters or words.<br/> + For example, to search for samples starting with 'mysample' use 'mysample%' as the search string. + </div></div> %if results: <div class="form-row"><label><i>${results}</i></label> + <div class="toolParamHelp" style="clear: both;"> + The search results are sorted by the date the samples where created. + </div></div> %endif <div class="form-row"> %if samples: %for s in samples: <div class="form-row"> - <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}"><label>Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</label></a> + + Sample: ${s.name} | Barcode: ${s.bar_code}<br/> + State: ${s.current_state().name}<br/> + Datasets: <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(s.id))}">${s.transferred_dataset_files()}/${len(s.datasets)}</a><br/> %if cntrller == 'requests_admin': <i>User: ${s.request.user.email}</i> %endif - <div class="toolParamHelp" style="clear: both;"> - Sample: ${s.name}<br/> - Barcode: ${s.bar_code}<br/> - State: ${s.current_state().name} - </div> + <div class="toolParamHelp" style="clear: both;"> + <a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}">Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</a> + </div> + </div><br/> %endfor %endif - </div></form></div> --- /dev/null +++ b/templates/requests/find_index.mako @@ -0,0 +1,16 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="requests" + self.message_box_visible=False +%> +</%def> + +<%def name="center_panel()"> + + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${h.url_for( controller="requests_common", action="find" )}"></iframe> + +</%def> --- a/lib/galaxy/web/controllers/requests.py +++ b/lib/galaxy/web/controllers/requests.py @@ -135,6 +135,11 @@ class Requests( BaseController ): @web.require_login( "create/submit sequencing requests" ) def index( self, trans ): return trans.fill_template( "requests/index.mako" ) + + @web.expose + @web.require_login( "create/submit sequencing requests" ) + def find_index( self, trans ): + return trans.fill_template( "requests/find_index.mako" ) @web.expose @web.require_login( "create/submit sequencing requests" ) --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1256,6 +1256,25 @@ class RequestsCommon( BaseController, Us # # Find sequencing requests & samples # + def __find_widgets(self, trans, **kwd): + params = util.Params( kwd ) + request_states = SelectField('request_states', multiple=True, display="checkboxes") + sel_op = kwd.get('request_states', trans.app.model.Request.states.SUBMITTED) + for i, s in trans.app.model.Request.states.items(): + if s in sel_op: + request_states.add_option(s, s, True) + else: + request_states.add_option(s, s) + search_type = SelectField('search_type') + sel_op = kwd.get('search_type', 'sample name') + for s in ['sample name', 'barcode', 'dataset']: + if s in sel_op: + search_type.add_option(s, s, True) + else: + search_type.add_option(s, s) + search_box = TextField('search_box', 50, kwd.get('search_box', '')) + return request_states, search_type, search_box + @web.expose @web.require_admin def find( self, trans, **kwd ): @@ -1263,26 +1282,31 @@ class RequestsCommon( BaseController, Us cntrller = params.get( 'cntrller', 'requests' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - search_string = kwd.get( 'search_string', '' ) - search_type = params.get( 'search_type', '' ) - if params.get( 'request_state', 'In Progress' ) == 'Both': - request_states = ['In Progress', 'Complete'] - else: - request_states = [params.get( 'request_state', 'In Progress' )] - - samples_list = [] results = '' - if params.get('go_button', '') == 'Go': - if search_type == 'bar_code': + if params.get('go_button', '') == 'Find': + search_string = kwd.get( 'search_box', '' ) + search_type = params.get( 'search_type', '' ) + request_states = params.get( 'request_states', '' ) + samples = [] + if search_type == 'barcode': samples = trans.sa_session.query( trans.app.model.Sample ) \ .filter( and_( trans.app.model.Sample.table.c.deleted==False, trans.app.model.Sample.table.c.bar_code.like(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ .all() - elif search_type == 'name': + elif search_type == 'sample name': samples = trans.sa_session.query( trans.app.model.Sample ) \ .filter( and_( trans.app.model.Sample.table.c.deleted==False, - trans.app.model.Sample.table.c.name.like(search_string) ) )\ + trans.app.model.Sample.table.c.name.ilike(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ + .all() + elif search_type == 'dataset': + samples = trans.sa_session.query( trans.app.model.Sample ) \ + .filter( and_( trans.app.model.Sample.table.c.deleted==False, + trans.app.model.SampleDataset.table.c.sample_id==trans.app.model.Sample.table.c.id, + trans.app.model.SampleDataset.table.c.name.ilike(search_string) ) )\ + .order_by( trans.app.model.Sample.table.c.create_time.desc())\ .all() if cntrller == 'requests': for s in samples: @@ -1295,11 +1319,12 @@ class RequestsCommon( BaseController, Us if not s.request.deleted \ and s.request.state() in request_states: samples_list.append(s) - results = 'There are %i sequencing requests matching the search parameters.' % len(samples_list) + results = 'There are %i sample(s) matching the search parameters.' % len(samples_list) + request_states, search_type, search_box = self.__find_widgets(trans, **kwd) return trans.fill_template( '/requests/common/find.mako', - cntrller=cntrller, - samples=samples_list, - results=results ) + cntrller=cntrller, request_states=request_states, + samples=samples_list, search_type=search_type, + results=results, search_box=search_box ) --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -82,7 +82,7 @@ <% menu_options = [ [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], - [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ], + [ 'Find Samples', h.url_for( controller='/requests', action='find_index' ) ], [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] ] tab( "lab", "Lab", None, menu_options=menu_options )

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galaxy-dist commit eb75925d4b97: lims: find samples
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283369397 14400 # Node ID eb75925d4b9705ab8722cab41c321bf15a4b2359 # Parent e37392b073d89af5aea5e6206e9827ea6ad3f190 lims: find samples - bug fix: filtering results by only one state is working - UI improvements --- a/templates/requests/common/find.mako +++ b/templates/requests/common/find.mako @@ -83,18 +83,19 @@ </div> %if results: <div class="form-row"> - <label><i>${results}</i></label> - <div class="toolParamHelp" style="clear: both;"> - The search results are sorted by the date the samples where created. - </div> + <label><i>${results}</i></label> + %if samples: + <div class="toolParamHelp" style="clear: both;"> + The search results are sorted by the date the samples where created. + </div> + %endif </div> %endif <div class="form-row"> %if samples: %for s in samples: <div class="form-row"> - - Sample: ${s.name} | Barcode: ${s.bar_code}<br/> + Sample: <b>${s.name}</b> | Barcode: ${s.bar_code}<br/> State: ${s.current_state().name}<br/> Datasets: <a href="${h.url_for(controller='requests_common', cntrller=cntrller, action='show_datatx_page', sample_id=trans.security.encode_id(s.id))}">${s.transferred_dataset_files()}/${len(s.datasets)}</a><br/> %if cntrller == 'requests_admin': @@ -103,7 +104,6 @@ <div class="toolParamHelp" style="clear: both;"><a href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(s.request.id))}">Sequencing request: ${s.request.name} | Type: ${s.request.type.name} | State: ${s.request.state()}</a></div> - </div><br/> %endfor --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1287,7 +1287,7 @@ class RequestsCommon( BaseController, Us if params.get('go_button', '') == 'Find': search_string = kwd.get( 'search_box', '' ) search_type = params.get( 'search_type', '' ) - request_states = params.get( 'request_states', '' ) + request_states = util.listify( params.get( 'request_states', '' ) ) samples = [] if search_type == 'barcode': samples = trans.sa_session.query( trans.app.model.Sample ) \

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galaxy-dist commit 2ba0fe1297a8: lims : UI improvements to the request info page
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283372432 14400 # Node ID 2ba0fe1297a8a31f99c412f05046ec7c2f749798 # Parent 12c032ebc303060b838448ad8f6e0da96cacb631 lims : UI improvements to the request info page --- a/lib/galaxy/web/controllers/requests_common.py +++ b/lib/galaxy/web/controllers/requests_common.py @@ -1138,17 +1138,6 @@ class RequestsCommon( BaseController, Us request = trans.sa_session.query( trans.app.model.Request ).get( id ) # list of widgets to be rendered on the request form request_details = [] - # main details - request_details.append(dict(label='Description', - value=request.desc, - helptext='')) - request_details.append(dict(label='Date created', - value=request.create_time, - helptext='')) - request_details.append(dict(label='Date updated', - value=request.update_time, - helptext='')) - # form fields for index, field in enumerate(request.type.request_form.fields): if field['required']: --- a/templates/requests/common/show_request.mako +++ b/templates/requests/common/show_request.mako @@ -225,6 +225,15 @@ function showContent(vThis) <tbody><tr><td valign="top" width="50%"> + <div class="form-row"> + <label>Description:</label> + %if request.desc: + ${request.desc} + %else: + <i>None</i> + %endif + </div> + <div style="clear: both"></div> %for index, rd in enumerate(request_details): <div class="form-row"><label>${rd['label']}:</label> @@ -242,6 +251,14 @@ function showContent(vThis) %endfor </td><td valign="top" width="50%"> + <div class="form-row"> + <label>Date created:</label> + ${request.create_time} + </div> + <div class="form-row"> + <label>Date updated:</label> + ${request.update_time} + </div><div class="form-row"><label>Email notification recipient(s):</label><% emails = ', '.join(request.notification['email']) %>

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galaxy-dist commit f41f4ace420a: For UI tab generation, only create link if there is an href.
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1283364901 14400 # Node ID f41f4ace420a58e7316fbeddacd301ff6d5dfaf1 # Parent 5f87abcf4854c6e5603a5b937865d3e8bdc9190d For UI tab generation, only create link if there is an href. --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -26,7 +26,12 @@ if not visible: style = "display: none;" %> - <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a> + <td class="${cls}" style="${style}"> + %if href: + <a target="${target}" href="${href}">${display}</a> + %else: + ${display} + %endif %if menu_options: <div class="submenu"><ul>

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galaxy-dist commit 397241b761ab: Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b .
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1283346658 14400 # Node ID 397241b761abe9a0cdad1f815e0a83328e3a665c # Parent c79aa66e7fd2b69c73a1937a0a58aec2f98e06e2 Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b . --- a/tools/extract/extract_genomic_dna.xml +++ b/tools/extract/extract_genomic_dna.xml @@ -43,12 +43,12 @@ </test><test> - <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /><param name="out_format" value="interval"/><output name="out_file1" file="extract_genomic_dna_out4.gff" /></test><test> - <param name="input" value="gff_filtering_out1.gff" dbkey="mm9" ftype="gff" /> + <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" /><param name="out_format" value="fasta"/><output name="out_file1" file="extract_genomic_dna_out5.fasta" /></test>

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galaxy-dist commit 37cbea4bf8c7: Added tool_conf.xml.main with BAM-to-SAM tool
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1283350216 14400 # Node ID 37cbea4bf8c7995eea2b202fe3fcfbc72d0307a7 # Parent 09a684e9e0d42a3704e0093a15e54ad339da6329 Added tool_conf.xml.main with BAM-to-SAM tool --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -327,6 +327,7 @@ <tool file="samtools/sam_bitwise_flag_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" />

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galaxy-dist commit 09a684e9e0d4: Added BAM-to-SAM tool
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1283348652 14400 # Node ID 09a684e9e0d42a3704e0093a15e54ad339da6329 # Parent 397241b761abe9a0cdad1f815e0a83328e3a665c Added BAM-to-SAM tool --- /dev/null +++ b/test-data/bam_to_sam_out1.sam @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 --- /dev/null +++ b/tools/samtools/bam_to_sam.py @@ -0,0 +1,66 @@ +#!/usr/bin/env python +""" +Converts BAM data to sorted SAM data. +usage: bam_to_sam.py [options] + --input1: SAM file to be converted + --output1: output dataset in bam format +""" + +import optparse, os, sys, subprocess, tempfile, shutil +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse +#from galaxy import util + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) + parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + ( options, args ) = parser.parse_args() + + tmp_dir = tempfile.mkdtemp() + try: + # exit if input file empty + if os.path.getsize( options.input1 ) == 0: + raise Exception, 'Initial BAM file empty' + # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). + command = 'samtools view -o %s %s' % ( options.output1, options.input1 ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) ) + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + # check that there are results in the output file + if os.path.getsize( options.output1 ) > 0: + sys.stdout.write( 'BAM file converted to SAM' ) + else: + stop_err( 'The output file is empty, there may be an error with your input file.' ) + +if __name__=="__main__": __main__() --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -286,6 +286,7 @@ <tool file="samtools/sam_bitwise_flag_filter.xml" /><tool file="samtools/sam2interval.xml" /><tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" /> --- /dev/null +++ b/tools/samtools/bam_to_sam.xml @@ -0,0 +1,37 @@ +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.0"> + <description>converts BAM format to SAM format</description> + <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command> + <inputs> + <param name="input1" type="data" format="bam" label="BAM File to Convert" /> + </inputs> + <outputs> + <data name="output1" format="sam" /> + </outputs> + <tests> + <test> +  + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="bam_to_sam_out1.sam" /> + </test> + <test> +  + <param name="input1" value="3.bam" ftype="bam" /> + <param name="output1" file="bam_to_sam_out2.sam" /> + </test> + </tests> + <help> + +**What it does** + +This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. + +.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml + + </help> +</tool> --- /dev/null +++ b/test-data/bam_to_sam_out2.sam @@ -0,0 +1,10 @@ +HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27

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galaxy-dist commit 5f87abcf4854: fix for the menu item bug intriduced in changeset 4223:03d06d05bf62
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1283357789 14400 # Node ID 5f87abcf4854c6e5603a5b937865d3e8bdc9190d # Parent 37cbea4bf8c7995eea2b202fe3fcfbc72d0307a7 fix for the menu item bug intriduced in changeset 4223:03d06d05bf62 now the Lab menu appears correctly for sample tracking users --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -74,18 +74,20 @@ ## Lab menu. %if trans.user and trans.user.accessible_request_types(trans): - menu_options = [ - [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], - [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ], - [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" )}, "galaxy_main" ], - ] - tab( "lab", "Lab", None, menu_options=menu_options ) + <% + menu_options = [ + [ 'Sequencing Requests', h.url_for( controller='/requests', action='index' ) ], + [ 'Find Samples', h.url_for( controller='/requests_common', action='find' ) ], + [ 'Help', app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] + ] + tab( "lab", "Lab", None, menu_options=menu_options ) + %> %endif ## Visualization menu. %if app.config.get_bool( 'enable_tracks', False ): <% - menu_options = [ + menu_options = [ ['New Track Browser', h.url_for( controller='/tracks', action='index' ) ], ['Saved Visualizations', h.url_for( controller='/visualization', action='list' ) ] ]

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galaxy-dist commit ce299d78b567: Tweaks to lines_diff in 2 rg tests to account for different versions of R and plink
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283301008 14400 # Node ID ce299d78b5670aa548b9ecad47754f6b5ce8584f # Parent 03d06d05bf62a6444f1a652910708fde17fa189b Tweaks to lines_diff in 2 rg tests to account for different versions of R and plink --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -42,7 +42,7 @@ <param name='chrom_col' value='1' /><param name='offset_col' value='2' /><param name='grey' value='0' /> - <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='30'> + <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='40'><extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size" delta = "10000"/><extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size" --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -32,8 +32,8 @@ <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "5000"/><extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /> - <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" /> - <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" /> + <extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/> + <extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/><extra_files type="file" name='tinywga.imendel' value="rgtestouts/rgQC/tinywga.imendel" compare="diff"/><extra_files type="file" name='tinywga.imiss' value="rgtestouts/rgQC/tinywga.imiss" compare="diff" /><extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" />

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galaxy-dist commit c79aa66e7fd2: Another small tweak - no idea what combination of plink and other dependencies
by commits-noreply＠bitbucket.org 09 Sep '10

09 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User fubar: ross Lazarus at gmail period com # Date 1283313090 14400 # Node ID c79aa66e7fd2b69c73a1937a0a58aec2f98e06e2 # Parent ce299d78b5670aa548b9ecad47754f6b5ce8584f Another small tweak - no idea what combination of plink and other dependencies will have on lines_diff at other sites...but buildbot seems fussy Still missing scipy and haploview seems unhappy too. --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -30,7 +30,7 @@ <param name='out_prefix' value='rgQCtest1' /><output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='280'><extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "5000"/> - <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="10"/> + <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/><extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" /><extra_files type="file" name='tinywga.het' value="rgtestouts/rgQC/tinywga.het" compare="diff" lines_diff="90"/><extra_files type="file" name='tinywga.hwe' value="rgtestouts/rgQC/tinywga.hwe" compare="diff" lines_diff="90"/> @@ -39,13 +39,13 @@ <extra_files type="file" name='tinywga.lmendel' value="rgtestouts/rgQC/tinywga.lmendel" compare="diff" /><extra_files type="file" name='tinywga.lmiss' value="rgtestouts/rgQC/tinywga.lmiss" compare="diff" /><extra_files type="file" name='tinywga_All_3x3.pdf' value="rgtestouts/rgQC/tinywga_All_3x3.pdf" compare="sim_size" delta="5000"/> - <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" /> + <extra_files type="file" name='ldp_tinywga.bed' value="rgtestouts/rgQC/ldp_tinywga.bed" compare="diff" lines_diff="10" /><extra_files type="file" name='ldp_tinywga.bim' value="rgtestouts/rgQC/ldp_tinywga.bim" compare="sim_size" delta="1000" /><extra_files type="file" name='ldp_tinywga.fam' value="rgtestouts/rgQC/ldp_tinywga.fam" compare="diff" /> - <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="17"/> + <extra_files type="file" name='ldp_tinywga.log' value="rgtestouts/rgQC/ldp_tinywga.log" compare="diff" lines_diff="20"/><extra_files type="file" name='Ranked_Marker_HWE.xls' value="rgtestouts/rgQC/Ranked_Marker_HWE.xls" compare="diff" /><extra_files type="file" name='Ranked_Marker_MAF.xls' value="rgtestouts/rgQC/Ranked_Marker_MAF.xls" compare="diff" /> - <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" /> + <extra_files type="file" name='Ranked_Marker_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Marker_Missing_Genotype.xls" compare="diff" lines_diff="5"/><extra_files type="file" name='Ranked_Subject_Missing_Genotype.xls' value="rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls" compare="diff" lines_diff="10"/><extra_files type="file" name='tinywga_fracmiss_cum.jpg' value="rgtestouts/rgQC/tinywga_fracmiss_cum.jpg" compare="sim_size" delta = "1000"/><extra_files type="file" name='tinywga_fracmiss_cum.pdf' value="rgtestouts/rgQC/tinywga_fracmiss_cum.pdf" compare="sim_size" delta = "1000"/>

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galaxy-commits September 2010