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commit/galaxy-central: jgoecks: Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links.
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c0d6d17fc7db/ changeset: r5122:c0d6d17fc7db user: jgoecks date: 2011-02-24 21:24:52 summary: Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links. affected #: 5 files (6.0 KB) --- a/lib/galaxy/jobs/__init__.py Thu Feb 24 15:23:21 2011 -0500 +++ b/lib/galaxy/jobs/__init__.py Thu Feb 24 15:24:52 2011 -0500 @@ -505,10 +505,14 @@ return job_context = ExpressionContext( dict( stdout = stdout, stderr = stderr ) ) job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) - def file_in_dir( file_path, a_dir ): - """ Returns true if file is in directory. """ - abs_file_path = os.path.abspath( file_path ) - return os.path.split( abs_file_path )[0] == os.path.abspath( a_dir ) + def in_directory( file, directory ): + # Make both absolute. + directory = os.path.realpath( directory ) + file = os.path.realpath( file ) + + #Return true, if the common prefix of both is equal to directory + #e.g. /a/b/c/d.rst and directory is /a/b, the common prefix is /a/b + return os.path.commonprefix( [ file, directory ] ) == directory for dataset_assoc in job.output_datasets + job.output_library_datasets: context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur @@ -523,7 +527,7 @@ if hda_tool_output and hda_tool_output.from_work_dir: # Copy from working dir to HDA. source_file = os.path.join( os.path.abspath( self.working_directory ), hda_tool_output.from_work_dir ) - if file_in_dir( source_file, self.working_directory ): + if in_directory( source_file, self.working_directory ): try: shutil.move( source_file, dataset.file_name ) log.debug( "finish(): Moved %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) --- a/tools/ngs_rna/tophat_wrapper.py Thu Feb 24 15:23:21 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.py Thu Feb 24 15:24:52 2011 -0500 @@ -30,6 +30,10 @@ parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) + parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' ) + parser.add_option( '', '--allow-indels', action="store_true", help='Allow indel search. Indel search is disabled by default.' ) + parser.add_option( '', '--max-insertion-length', dest='max_insertion_length', help='The maximum insertion length. The default is 3.' ) + parser.add_option( '', '--max-deletion-length', dest='max_deletion_length', help='The maximum deletion length. The default is 3.' ) # Options for supplying own junctions parser.add_option( '-G', '--GTF', dest='gene_model_annotations', help='Supply TopHat with a list of gene model annotations. \ @@ -115,8 +119,7 @@ index_path = options.index_path # Build tophat command. - tmp_output_dir = tempfile.mkdtemp() - cmd = 'tophat -o %s %s %s %s' + cmd = 'tophat %s %s %s' reads = options.input1 if options.input2: reads += ' ' + options.input2 @@ -124,7 +127,7 @@ if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist if options.settings == 'preSet': - cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + cmd = cmd % ( opts, index_path, reads ) else: try: if int( options.min_anchor_length ) >= 3: @@ -144,6 +147,13 @@ opts += ' -j %s' % options.raw_juncs if options.no_novel_juncs: opts += ' --no-novel-juncs' + if options.library_type: + opts += ' --library-type %s' % options.library_type + if options.allow_indels: + # Max options do not work for Tophat v1.2.0, despite documentation to the contrary. + opts += ' --allow-indels' + #opts += ' --allow-indels --max-insertion-length %i --max-deletion-length %i' % ( int( options.max_insertion_length ), int( options.max_deletion_length ) ) + # Search type options. if options.coverage_search: @@ -166,23 +176,21 @@ opts += ' --min-segment-intron %d' % int(options.min_segment_intron) if options.max_segment_intron: opts += ' --max-segment-intron %d' % int(options.max_segment_intron) - cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + cmd = cmd % ( opts, index_path, reads ) except Exception, e: # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) print cmd # Run try: - tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_out = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp_out, 'wb' ) - tmp_err = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stdout=tmp_stdout, stderr=tmp_stderr ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) returncode = proc.wait() tmp_stderr.close() # get stderr, allowing for case where it's very large @@ -202,17 +210,11 @@ raise Exception, stderr # TODO: look for errors in program output. - - # Copy output files from tmp directory to specified files. - shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) - shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file ) except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) # Clean up temp dirs if os.path.exists( tmp_index_dir ): shutil.rmtree( tmp_index_dir ) - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() --- a/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 15:23:21 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 15:24:52 2011 -0500 @@ -39,6 +39,14 @@ --max-segment-intron $singlePaired.sParams.max_segment_intron --seg-mismatches=$singlePaired.sParams.seg_mismatches --seg-length=$singlePaired.sParams.seg_length + --library-type=$singlePaired.sParams.library_type + + ## Indel search. + #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes": + --allow-indels + --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length + --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length + #end if ## Supplying junctions parameters. #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": @@ -90,6 +98,14 @@ --max-segment-intron $singlePaired.pParams.max_segment_intron --seg-mismatches=$singlePaired.pParams.seg_mismatches --seg-length=$singlePaired.pParams.seg_length + --library-type=$singlePaired.pParams.library_type + + ## Indel search. + #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes": + --allow-indels + --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length + --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length + #end if ## Supplying junctions parameters. #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": @@ -157,10 +173,26 @@ <when value="preSet" /><when value="full"> + <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> + <option value="fr-unstranded">FR Unstranded</option> + <option value="fr-firststrand">FR First Strand</option> + <option value="fr-secondstrand">FR Second Strand</option> + </param><param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /><param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -247,11 +279,27 @@ <when value="preSet" /><when value="full"> + <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> + <option value="fr-unstranded">FR Unstranded</option> + <option value="fr-firststrand">FR First Strand</option> + <option value="fr-secondstrand">FR Second Strand</option> + </param><param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /><param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -329,8 +377,28 @@ </inputs><outputs> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> + <filter> + ( + ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and + ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or + ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and + ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) + ) + </filter> + </data> + <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> + <filter> + ( + ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and + ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or + ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and + ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) + ) + </filter> + </data> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"/> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"/></outputs><tests> @@ -367,7 +435,7 @@ <test><param name="genomeSource" value="history"/> @@ -375,6 +443,7 @@ <param name="sPaired" value="single"/><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="sSettingsType" value="full"/> + <param name="library_type" value="FR Unstranded"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/> @@ -386,6 +455,9 @@ <param name="max_segment_intron" value="500000" /><param name="seg_mismatches" value="2"/><param name="seg_length" value="25"/> + <param name="allow_indel_search" value="Yes"/> + <param name="max_insertion_length" value="3"/> + <param name="max_deletion_length" value="3"/><param name="use_junctions" value="Yes" /><param name="use_annotations" value="No" /><param name="use_juncs" value="No" /> @@ -398,6 +470,8 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> + <output name="insertions" file="tophat_out3i.bed" ftype="bed"/> + <output name="deletions" file="tophat_out3d.bed" ftype="bed"/><output name="junctions" file="tophat_out3j.bed" ftype="bed" /><output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" ftype="bam" /></test> @@ -414,6 +488,7 @@ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="full"/> + <param name="library_type" value="FR Unstranded"/><param name="mate_std_dev" value="20"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/> @@ -426,6 +501,7 @@ <param name="max_segment_intron" value="500000" /><param name="seg_mismatches" value="2"/><param name="seg_length" value="25"/> + <param name="allow_indel_search" value="No"/><param name="use_junctions" value="Yes" /><param name="use_annotations" value="No" /><param name="use_juncs" value="No" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Fix bed_to_bigBed test
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1a544e327b3d/ changeset: r5121:1a544e327b3d user: kanwei date: 2011-02-24 21:23:21 summary: Fix bed_to_bigBed test affected #: 2 files (18 bytes) --- a/buildbot_setup.sh Thu Feb 24 15:07:46 2011 -0500 +++ b/buildbot_setup.sh Thu Feb 24 15:23:21 2011 -0500 @@ -109,7 +109,7 @@ fi done -# for wig_to_bigWig +# for wig_to_bigWig and bed_to_bigBed if [ ! -f "tool-data/shared/ucsc/chrom/hg17.len" -a -f "test-data/wig_to_bigwig_hg17.len" ]; then mkdir -p tool-data/shared/ucsc/chrom cp test-data/wig_to_bigwig_hg17.len tool-data/shared/ucsc/chrom/hg17.len --- a/tools/filters/bed_to_bigbed.xml Thu Feb 24 15:07:46 2011 -0500 +++ b/tools/filters/bed_to_bigbed.xml Thu Feb 24 15:23:21 2011 -0500 @@ -31,7 +31,7 @@ </outputs><tests><test> - <param name="input1" value="7.bed" dbkey="hg18" /> + <param name="input1" value="7.bed" dbkey="hg17" /><param name="settingsType" value="full" /><param name="blockSize" value="256" /><param name="itemsPerSlot" value="512" /> @@ -39,7 +39,7 @@ <output name="out_file1" file="7.bigbed"/></test><test> - <param name="input1" value="7.bed" dbkey="hg18" /> + <param name="input1" value="7.bed" dbkey="hg17" /><param name="settingsType" value="preset" /><output name="out_file1" file="7.bigbed"/></test> 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: kanwei: Fix BLAST+ test
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fb51941391ed/ changeset: r5120:fb51941391ed user: kanwei date: 2011-02-24 21:07:46 summary: Fix BLAST+ test affected #: 1 file (1 byte) --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Feb 24 12:27:37 2011 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Feb 24 15:07:46 2011 -0500 @@ -1,7 +1,7 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.8"><description>Search translated nucleotide database with protein query sequence(s)</description><command interpreter="python">hide_stderr.py -# The command is a Cheetah template which allows some Python based syntax. +## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces tblastn -query "$query" 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: kanwei: Fix debugging output on BLASTX+ failure
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd3c21ebfa4a/ changeset: r5119:dd3c21ebfa4a user: kanwei date: 2011-02-24 18:27:37 summary: Fix debugging output on BLASTX+ failure affected #: 1 file (164 bytes) --- a/tools/ncbi_blast_plus/hide_stderr.py Thu Feb 24 12:16:33 2011 -0500 +++ b/tools/ncbi_blast_plus/hide_stderr.py Thu Feb 24 12:27:37 2011 -0500 @@ -23,6 +23,13 @@ #Avoid using shell=True when we call subprocess to ensure if the Python #script is killed, so too is the BLAST process. try: + words = [] + for w in sys.argv[1:]: + if " " in w: + words.append('"%s"' % w) + else: + words.append(w) + cmd = " ".join(words) child = subprocess.Popen(sys.argv[1:], stdout=subprocess.PIPE, stderr=subprocess.PIPE) except Exception, err: 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: rc: Adding ftype attribute to vcf tool tests
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/07275d9052af/ changeset: r5118:07275d9052af user: rc date: 2011-02-24 18:16:33 summary: Adding ftype attribute to vcf tool tests affected #: 3 files (142 bytes) --- a/lib/galaxy/tools/parameters/basic.py Thu Feb 24 09:17:50 2011 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Thu Feb 24 12:16:33 2011 -0500 @@ -202,7 +202,7 @@ except: raise ValueError( "An integer is required" ) elif self.value is None: - raise ValueError( "The settings for this field require a 'value' setting and optionally a default value which must be an integer" ) + raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name ) self.min = elem.get( 'min' ) self.max = elem.get( 'max' ) if self.min: --- a/tools/vcf_tools/annotate.xml Thu Feb 24 09:17:50 2011 -0500 +++ b/tools/vcf_tools/annotate.xml Thu Feb 24 12:16:33 2011 -0500 @@ -31,15 +31,15 @@ </outputs><tests><test> - <param name="input1" value="test.small.vcf" /> + <param name="input1" value="test.small.vcf" ftype="vcf" /><param name="annotate" value="dbsnp" /> - <param name="input2" value="dbsnp.small.vcf" /> + <param name="input2" value="dbsnp.small.vcf" ftype="vcf" /><output name="output" file="test_annotated_dbsnp.vcf" lines_diff="6" ftype="vcf" /></test><test> - <param name="input1" value="test.small.vcf" /> + <param name="input1" value="test.small.vcf" ftype="vcf" /><param name="annotate" value="hapmap" /> - <param name="input2" value="hapmap.small.vcf" /> + <param name="input2" value="hapmap.small.vcf" ftype="vcf" /><output name="output" file="test_annotated_hapmap.vcf" lines_diff="6" ftype="vcf" /></test></tests> --- a/tools/vcf_tools/intersect.xml Thu Feb 24 09:17:50 2011 -0500 +++ b/tools/vcf_tools/intersect.xml Thu Feb 24 12:16:33 2011 -0500 @@ -41,23 +41,23 @@ </outputs><tests><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="none" /><output name="output" file="1_2_intersect_priority_0.vcf" lines_diff="2" ftype="vcf" /></test><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="first_file" /><output name="output" file="1_2_intersect_priority_1.vcf" lines_diff="2" ftype="vcf" /></test><test> - <param name="input1" value="1.vcf" /> + <param name="input1" value="1.vcf" ftype="vcf" /><param name="format" value="vcf" /> - <param name="input2" value="2.vcf" /> + <param name="input2" value="2.vcf" ftype="vcf" /><param name="priority_file" value="second_file" /><output name="output" file="1_2_intersect_priority_2.vcf" lines_diff="2" ftype="vcf" /></test> 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 functional test outputs for v1.2.0 of Tophat.
by Bitbucket 24 Feb '11

24 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5fca3e76c2f4/ changeset: r5117:5fca3e76c2f4 user: jgoecks date: 2011-02-24 15:17:50 summary: Update functional test outputs for v1.2.0 of Tophat. affected #: 4 files (0 bytes) --- a/test-data/tophat_out1j.bed Wed Feb 23 14:53:54 2011 -0500 +++ b/test-data/tophat_out1j.bed Thu Feb 24 09:17:50 2011 -0500 @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 180 400 JUNC00000001 26 + 180 400 255,0,0 2 70,50 0,170 test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- a/test-data/tophat_out2j.bed Wed Feb 23 14:53:54 2011 -0500 +++ b/test-data/tophat_out2j.bed Thu Feb 24 09:17:50 2011 -0500 @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 180 402 JUNC00000001 49 + 180 402 255,0,0 2 70,52 0,170 test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- a/test-data/tophat_out3j.bed Wed Feb 23 14:53:54 2011 -0500 +++ b/test-data/tophat_out3j.bed Thu Feb 24 09:17:50 2011 -0500 @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 400 JUNC00000001 24 + 180 400 255,0,0 2 70,50 0,170 +test_chromosome 180 400 JUNC00000001 26 + 180 400 255,0,0 2 70,50 0,170 test_chromosome 349 550 JUNC00000002 22 + 349 550 255,0,0 2 51,50 0,151 --- a/test-data/tophat_out4j.bed Wed Feb 23 14:53:54 2011 -0500 +++ b/test-data/tophat_out4j.bed Thu Feb 24 09:17:50 2011 -0500 @@ -1,3 +1,3 @@ track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 180 402 JUNC00000001 49 + 180 402 255,0,0 2 70,52 0,170 test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 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: natefoo: When comparing bam files in the test framework, convert them to sam for comparison.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/93783833e6b1/ changeset: r5116:93783833e6b1 user: natefoo date: 2011-02-23 20:53:54 summary: When comparing bam files in the test framework, convert them to sam for comparison. affected #: 2 files (949 bytes) --- a/test/base/twilltestcase.py Wed Feb 23 14:01:58 2011 -0500 +++ b/test/base/twilltestcase.py Wed Feb 23 14:53:54 2011 -0500 @@ -1,7 +1,7 @@ import pkg_resources pkg_resources.require( "twill==0.9" ) -import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil +import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, tarfile, zipfile, tempfile, re, shutil, subprocess from itertools import * import twill @@ -633,6 +633,9 @@ try: if attributes is None: attributes = {} + if attributes.get( 'ftype', None ) == 'bam': + local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) + local_name = local_fh.name compare = attributes.get( 'compare', 'diff' ) extra_files = attributes.get( 'extra_files', None ) if compare == 'diff': @@ -658,6 +661,17 @@ finally: os.remove( temp_name ) + def _bam_to_sam( self, local_name, temp_name ): + temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) + fd, temp_temp = tempfile.mkstemp( suffix='.sam', prefix='history_bam_converted_to_sam_' ) + os.close( fd ) + p = subprocess.Popen( args="samtools view %s -o %s" % ( local_name, temp_local.name ), shell=True ) + assert not p.wait(), 'Converting local (test-data) bam to sam failed' + p = subprocess.Popen( args="samtools view %s -o %s" % ( temp_name, temp_temp ), shell=True ) + assert not p.wait(), 'Converting history bam to sam failed' + os.remove( temp_name ) + return temp_local, temp_temp + def verify_extra_files_content( self, extra_files, hda_id ): files_list = [] for extra_type, extra_value, extra_name, extra_attributes in extra_files: --- a/test/functional/test_get_data.py Wed Feb 23 14:01:58 2011 -0500 +++ b/test/functional/test_get_data.py Wed Feb 23 14:53:54 2011 -0500 @@ -389,7 +389,7 @@ self.upload_file( '1.bam' ) hda = get_latest_hda() assert hda is not None, "Problem retrieving hda from database" - self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ) ) + self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ), attributes={ 'ftype' : 'bam' } ) self.check_history_for_string( '<span class="bam">bam</span>' ) # Make sure the Bam index was created assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam" 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: Initial commit of Mosaik and Freebayes.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7b2bc40bad02/ changeset: r5115:7b2bc40bad02 user: dannon date: 2011-02-23 20:01:58 summary: Initial commit of Mosaik and Freebayes. affected #: 5 files (302 bytes) --- a/tool_conf.xml.sample Wed Feb 23 13:54:06 2011 -0500 +++ b/tool_conf.xml.sample Wed Feb 23 14:01:58 2011 -0500 @@ -291,6 +291,7 @@ <tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /> + <tool file="sr_mapping/mosaik.xml"/></section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /> @@ -369,6 +370,7 @@ <tool file="human_genome_variation/beam.xml" /><tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /> + <tool file="human_genome_variation/freebayes.xml" /></section><section name="VCF Tools" id="vcf_tools"><tool file="vcf_tools/intersect.xml" /> --- a/tool_data_table_conf.xml.sample Wed Feb 23 13:54:06 2011 -0500 +++ b/tool_data_table_conf.xml.sample Wed Feb 23 14:01:58 2011 -0500 @@ -80,4 +80,9 @@ <columns>value, name, path</columns><file path="tool-data/ccat_configurations.loc" /></table> +  + <table name="mosaik_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/mosaik_index.loc" /> + </table></tables> 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: natefoo: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses.
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a6141e135830/ changeset: r5114:a6141e135830 user: natefoo date: 2011-02-23 19:54:06 summary: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses. affected #: 1 file (258 bytes) --- a/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 11:56:16 2011 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 13:54:06 2011 -0500 @@ -139,8 +139,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out1.u.sam bwa_wrapper_out1.sam --><param name="refGenomeSource" value="indexed" /> -  - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /><param name="source_select" value="pre_set" /> @@ -195,8 +194,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam --><param name="refGenomeSource" value="indexed" /> -  - <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /> + <param name="indices" value="phiX" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> 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: rc: Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476
by Bitbucket 23 Feb '11

23 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b54ef1e11b77/ changeset: r5113:b54ef1e11b77 user: rc date: 2011-02-23 17:56:16 summary: Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476 affected #: 2 files (890 bytes) --- a/lib/galaxy/web/controllers/requests_common.py Wed Feb 23 10:40:30 2011 -0500 +++ b/lib/galaxy/web/controllers/requests_common.py Wed Feb 23 11:56:16 2011 -0500 @@ -1432,7 +1432,11 @@ field_values = {} for field_index, field in enumerate( request.type.sample_form.fields ): field_name = field['name'] - field_value = util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), sample.values.content[ field_name ] ) ) + input_value = params.get( 'sample_%i_field_%i' % ( index, field_index ), sample.values.content[ field_name ] ) + if field['type'] == CheckboxField.__name__: + field_value = CheckboxField.is_checked( input_value ) + else: + field_value = util.restore_text( input_value ) field_values[ field_name ] = field_value library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, @@ -1504,8 +1508,13 @@ workflow_dict['mappings'][int(k[len(kwd_tag):])] = {'ds_tag':v} field_values = {} for field_index, field in enumerate( request.type.sample_form.fields ): - field_name = field['name'] - field_values[ field_name ] = util.restore_text( params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) ) + field_name = field['name'] + input_value = params.get( 'sample_%i_field_%i' % ( index, field_index ), '' ) + if field['type'] == CheckboxField.__name__: + field_value = CheckboxField.is_checked( input_value ) + else: + field_value = util.restore_text( input_value ) + field_values[ field_name ] = field_value library_select_field, folder_select_field = self.__build_library_and_folder_select_fields( trans=trans, user=request.user, sample_index=index, --- a/templates/requests/common/common.mako Wed Feb 23 10:40:30 2011 -0500 +++ b/templates/requests/common/common.mako Wed Feb 23 11:56:16 2011 -0500 @@ -591,7 +591,11 @@ %endfor </select> %elif field_type == 'CheckboxField': - <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/> + %if field_value is True: + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes" checked="checked"/><input type="hidden" name="sample_${index}_field_${field_index}" value="Yes"/> + %else: + <input type="checkbox" name="sample_${index}_field_${field_index}" value="Yes"/><input type="hidden" name="sample_${index}_field_${field_index}" value="Yes"/> + %endif %endif <div class="toolParamHelp" style="clear: both;"><i>${'('+field['required']+')' }</i> 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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