February 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: FreeBayes: make trace and failed alleles outputs optional.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/19c4b36d6981/ changeset: 19c4b36d6981 user: dan date: 2012-02-02 17:05:05 summary: FreeBayes: make trace and failed alleles outputs optional. affected #: 1 file diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 19c4b36d6981ab6d938167a7a6237f41425d6cb5 tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.1"> +<tool id="freebayes" name="FreeBayes" version="0.0.2"><requirements><requirement type="package" version="0.9.4">freebayes</requirement><requirement type="package">samtools</requirement> @@ -29,11 +29,17 @@ ##outputs --vcf "${output_vcf}" - --trace "${output_trace}" - --failed-alleles "${output_failed_alleles_bed}" ##advanced options #if str( $options_type.options_type_selector ) == "advanced": + #additional outputs + #if $options_type.output_trace_option: + --trace "${output_trace}" + #end if + #if $options_type.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + ##additional inputs #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": --targets "${options_type.target_limit_type.input_target_bed}" @@ -186,8 +192,13 @@ </when><when value="advanced"> - -  + +  + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> + + + <conditional name="target_limit_type"><param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"><option value="do_not_limit" selected="True">Do not limit</option> @@ -398,8 +409,12 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> + </data> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> + </data></outputs><tests><test> @@ -408,8 +423,8 @@ <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/><param name="options_type_selector" value="basic"/><output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> - <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> - <output name="output_failed_alleles_bed" file="empty_file.dat" /> + </test></tests><help> 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: dannon: History export - now works for a guest user.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/50bf77aa34c3/ changeset: 50bf77aa34c3 user: dannon date: 2012-02-02 16:51:13 summary: History export - now works for a guest user. affected #: 1 file diff -r 62c2a2f9142c11d1ae279ce3af395bd4fb0d4c52 -r 50bf77aa34c3689a122187d7ba9b55deb348df92 lib/galaxy/tools/actions/history_imp_exp.py --- a/lib/galaxy/tools/actions/history_imp_exp.py +++ b/lib/galaxy/tools/actions/history_imp_exp.py @@ -9,7 +9,7 @@ class ImportHistoryToolAction( ToolAction ): """Tool action used for importing a history to an archive. """ - def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): # # Create job. # @@ -20,43 +20,43 @@ job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters - trans.sa_session.add( job ) + trans.sa_session.add( job ) trans.sa_session.flush() #ensure job.id are available - + # # Setup job and job wrapper. # - + # Add association for keeping track of job, history relationship. - - # Use abspath because mkdtemp() does not, contrary to the documentation, + + # Use abspath because mkdtemp() does not, contrary to the documentation, # always return an absolute path. archive_dir = os.path.abspath( tempfile.mkdtemp() ) jiha = trans.app.model.JobImportHistoryArchive( job=job, archive_dir=archive_dir ) trans.sa_session.add( jiha ) job_wrapper = JobImportHistoryArchiveWrapper( job ) - + # # Add parameters to job_parameter table. # - + # Set additional parameters. incoming[ '__DEST_DIR__' ] = jiha.archive_dir for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) - + job.state = start_job_state #job inputs have been configured, restore initial job state trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - + return job, odict() class ExportHistoryToolAction( ToolAction ): """Tool action used for exporting a history to an archive. """ - + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): # # Get history to export. @@ -68,10 +68,10 @@ history = value del incoming[ history_param_name ] break - + if not history: raise Exception( 'There is no history to export.' ) - + # # Create the job and output dataset objects # @@ -79,22 +79,24 @@ job.session_id = trans.get_galaxy_session().id job.history_id = trans.history.id job.tool_id = tool.id - job.user_id = trans.user.id + if trans.user: + # If this is an actual user, run the job as that individual. Otherwise we're running as guest. + job.user_id = trans.user.id start_job_state = job.state #should be job.states.NEW job.state = job.states.WAITING #we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add( job ) - + # Create dataset that will serve as archive. archive_dataset = trans.app.model.Dataset() trans.sa_session.add( archive_dataset ) - + trans.sa_session.flush() #ensure job.id and archive_dataset.id are available trans.app.object_store.create( archive_dataset ) # set the object store id, create dataset (if applicable) - + # # Setup job and job wrapper. # - + # Add association for keeping track of job, history, archive relationship. jeha = trans.app.model.JobExportHistoryArchive( job=job, history=history, \ dataset=archive_dataset, \ @@ -104,23 +106,23 @@ job_wrapper = JobExportHistoryArchiveWrapper( job ) cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \ include_deleted=incoming[ 'include_deleted' ] ) - + # # Add parameters to job_parameter table. # - + # Set additional parameters. incoming[ '__HISTORY_TO_EXPORT__' ] = history.id incoming[ '__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' ] = cmd_line for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): job.add_parameter( name, value ) - + job.state = start_job_state #job inputs have been configured, restore initial job state trans.sa_session.flush() - - + + # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - + return job, odict() 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: dannon: History Size wasn't filtering out 'purged' datasets in the summary size, should now reflect accurate total on disk.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62c2a2f9142c/ changeset: 62c2a2f9142c user: dannon date: 2012-02-02 16:17:25 summary: History Size wasn't filtering out 'purged' datasets in the summary size, should now reflect accurate total on disk. affected #: 1 file diff -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 -r 62c2a2f9142c11d1ae279ce3af395bd4fb0d4c52 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -475,6 +475,7 @@ db_session = object_session( self ) rval = db_session.query( func.sum( db_session.query( HistoryDatasetAssociation.dataset_id, Dataset.total_size ).join( Dataset ) .filter( HistoryDatasetAssociation.table.c.history_id == self.id ) + .filter( Dataset.purged != True ) .distinct().subquery().c.total_size ) ).first()[0] if rval is None: rval = 0 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: Update version support information in Cuff* wrappers.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fdaa5c7d527/ changeset: 3fdaa5c7d527 user: jgoecks date: 2012-02-02 16:03:02 summary: Update version support information in Cuff* wrappers. affected #: 4 files diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> -  + <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffdiff" name="Cuffdiff" version="0.0.5"> -  + <description>find significant changes in transcript expression, splicing, and promoter use</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cufflinks" name="Cufflinks" version="0.0.5"> -  + <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements><requirement type="package">cufflinks</requirement> diff -r 93520b875b56905f50dd7de2b09bab189f2429ad -r 3fdaa5c7d5270564ea55b4c5997dde8c1c00a6e8 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> -  + <description>merge together several Cufflinks assemblies</description><requirements><requirement type="package">cufflinks</requirement> 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: Add num_threads parameter to cuffmerge wrapper script.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/93520b875b56/ changeset: 93520b875b56 user: jgoecks date: 2012-02-02 15:26:01 summary: Add num_threads parameter to cuffmerge wrapper script. affected #: 1 file diff -r 63bc8824dae5d8ab8cf45d86226fcd7f0508f46b -r 93520b875b56905f50dd7de2b09bab189f2429ad tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -25,6 +25,8 @@ parser = optparse.OptionParser() parser.add_option( '-g', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' ) parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + # Wrapper / Galaxy options. parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) @@ -74,6 +76,8 @@ cmd = "cuffmerge -o cm_output " # Add options. + if options.num_threads: + cmd += ( " -p %i" % int ( options.num_threads ) ) if options.ref_annotation: cmd += " -g %s " % options.ref_annotation if options.use_seq_data: 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: Add num-threads param to cuffdiff.
by Bitbucket 02 Feb '12

02 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63bc8824dae5/ changeset: 63bc8824dae5 user: jgoecks date: 2012-02-02 15:15:19 summary: Add num-threads param to cuffdiff. affected #: 1 file diff -r 724bbcc69c921ebe53b780d04f2699178201941e -r 63bc8824dae5d8ab8cf45d86226fcd7f0508f46b tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -5,7 +5,9 @@ <requirement type="package">cufflinks</requirement></requirements><command interpreter="python"> - cuffmerge_wrapper.py + cuffmerge_wrapper.py + + --num-threads="4" ## Use annotation reference? #if $annotation.use_ref_annotation == "Yes": 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: Add cuffmerge tool wrapper and functional test.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/724bbcc69c92/ changeset: 724bbcc69c92 user: jgoecks date: 2012-02-02 04:36:17 summary: Add cuffmerge tool wrapper and functional test. affected #: 5 files diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e test-data/cuffmerge_out1.gtf --- /dev/null +++ b/test-data/cuffmerge_out1.gtf @@ -0,0 +1,74 @@ +chr1 Cufflinks exon 4797974 4798063 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4798536 4798567 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4818665 4818730 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4820349 4820396 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4822392 4822462 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4827082 4827155 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4829468 4829569 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4831037 4831213 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4835044 4836816 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1"; +chr1 Cufflinks exon 4847775 4848057 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4857551 4857613 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4847775 4848057 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4857551 4857613 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4868108 4868213 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4876825 4876912 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4879538 4879683 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4880821 4880877 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4881996 4882150 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4883498 4883644 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4885015 4885086 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 4886437 4887987 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2"; +chr1 Cufflinks exon 3204563 3207049 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 3411783 3411982 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 3660633 3661579 . - . gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3"; +chr1 Cufflinks exon 4334224 4340172 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4341991 4342162 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4342283 4342918 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4350281 4350473 . - . gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4"; +chr1 Cufflinks exon 4481009 4482749 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4483181 4483547 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4483853 4483944 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4485217 4486023 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4486372 4486494 . - . gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5"; +chr1 Cufflinks exon 4763279 4764597 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4763279 4764597 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4774032 4774186 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4763279 4766882 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4767606 4767729 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4772649 4772814 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4774032 4774186 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 4775654 4775807 . - . gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6"; +chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7"; +chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8"; +chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9"; +chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10"; +chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11"; +chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12"; +chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13"; +chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14"; +chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15"; +chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16"; +chr1 Cufflinks exon 3192551 3192676 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17"; +chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18"; +chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19"; +chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20"; +chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21"; +chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22"; +chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23"; +chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24"; +chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25"; +chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26"; +chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27"; +chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28"; +chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29"; +chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30"; +chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31"; +chr1 Cufflinks exon 3201008 3201481 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32"; +chr1 Cufflinks exon 3201597 3201809 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33"; diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -406,6 +406,7 @@ <tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /><label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> diff -r 0f7670a67901587a939a93047b6b58bdb93f3516 -r 724bbcc69c921ebe53b780d04f2699178201941e tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -359,6 +359,7 @@ <tool file="ngs_rna/tophat_color_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <description>merge together several Cufflinks assemblies</description> + <requirements> + <requirement type="package">cufflinks</requirement> + </requirements> + <command interpreter="python"> + cuffmerge_wrapper.py + + ## Use annotation reference? + #if $annotation.use_ref_annotation == "Yes": + -g $annotation.reference_annotation + #end if + + ## Use sequence data? + #if $seq_data.use_seq_data == "Yes": + -s + #if $seq_data.seq_source.index_source == "history": + --ref_file=$seq_data.seq_source.ref_file + #else: + --ref_file="None" + #end if + --dbkey=${first_input.metadata.dbkey} + --index_dir=${GALAXY_DATA_INDEX_DIR} + #end if + + ## Outputs. + --merged-transcripts=${merged_transcripts} + + ## Inputs. + ${first_input} + #for $input_file in $input_files: + ${input_file.additional_input} + #end for + + </command> + <inputs> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> + <repeat name="input_files" title="Additional GTF Input Files"> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> + </repeat> + <conditional name="annotation"> + <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param format="gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when> + <when value="No"> + </when> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"></when> + <when value="Yes"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"></when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + </when> + </conditional> + </inputs> + + <outputs> + <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> + </outputs> + + <tests> +  + <test> + <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> + <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="use_ref_annotation" value="Yes"/> + <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="use_seq_data" value="No"/> + <output name="merged_transcripts" file="cuffmerge_out1.gtf"/> + </test> + </tests> + + <help> +**Cuffmerge Overview** + +Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 + +.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. + +.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge + +------ + +**Input format** + +Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) + +.. _Ensembl: http://www.ensembl.org + +------ + +**Outputs** + +Cuffmerge produces the following output files: + +Merged transcripts file: + +Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> +</tool> 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: 2 new changesets
by Bitbucket 01 Feb '12

01 Feb '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e5f7236a7e3a/ changeset: e5f7236a7e3a user: jgoecks date: 2012-02-01 22:47:32 summary: Change default sort for Pages list to update time. affected #: 1 file diff -r 315515ad52b04d15fe33476b7a33c1079712728c -r e5f7236a7e3ad4e6b6414beb875fc89206deebe7 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -23,7 +23,7 @@ title = "Pages" model_class = model.Page default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), https://bitbucket.org/galaxy/galaxy-central/changeset/0f7670a67901/ changeset: 0f7670a67901 user: jgoecks date: 2012-02-01 23:34:50 summary: To be compatible with distributed object store, use create() when adding data subsets for Trackster. affected #: 1 file diff -r e5f7236a7e3ad4e6b6414beb875fc89206deebe7 -r 0f7670a67901587a939a93047b6b58bdb93f3516 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -961,6 +961,7 @@ data_provider = data_provider_class( original_dataset=input_dataset, converted_dataset=converted_dataset, dependencies=deps ) + trans.app.object_store.create( new_dataset.dataset ) data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) # TODO: (a) size not working; (b) need to set peek. 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: Add overwrite param when setting metadata in Trackster data subsets.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/315515ad52b0/ changeset: 315515ad52b0 user: jgoecks date: 2012-02-01 21:27:53 summary: Add overwrite param when setting metadata in Trackster data subsets. affected #: 1 file diff -r a8eca62cd5304509a67e598d54d5203411aeb3df -r 315515ad52b04d15fe33476b7a33c1079712728c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -970,7 +970,7 @@ # 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 } ) + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset }, overwrite=False ) else: message = 'Attributes updated' new_dataset.set_meta() 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: Fix bug: when setting chromInfo, do not assume a fasta file exists.
by Bitbucket 01 Feb '12

01 Feb '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a8eca62cd530/ changeset: a8eca62cd530 user: jgoecks date: 2012-02-01 20:00:21 summary: Fix bug: when setting chromInfo, do not assume a fasta file exists. affected #: 1 file diff -r 7d97c594b1639bc16aba60ae8a0bf9a2798dbde8 -r a8eca62cd5304509a67e598d54d5203411aeb3df lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -193,12 +193,15 @@ incoming[ "chromInfo" ] = db_dataset.file_name else: # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + chrom_info = None if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] - build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) - chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name - else: + if 'fasta' in custom_build_dict: + build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) + chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name + + if not chrom_info: # Default to built-in build. chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) incoming[ "chromInfo" ] = chrom_info 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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