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

commit/galaxy-central: greg: When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store.
by Bitbucket 20 Jan '12

20 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2def96d78d18/ changeset: 2def96d78d18 user: greg date: 2012-01-20 16:26:54 summary: When uploading compressed files to a data library, remove the compressed file extension only if copying files into Galaxy's file store. affected #: 1 file diff -r c08d5e96b5dd8acdc976478cc3cf94b14af501bd -r 2def96d78d188597845d123555c49964b20f821b lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1052,14 +1052,17 @@ trans.sa_session.flush() return output def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): + link_data_only = params.get( 'link_data_only', 'copy_files' ) library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() - # Remove compressed file extensions, if any new_name = name - if new_name.endswith( '.gz' ): - new_name = new_name.rstrip( '.gz' ) - elif new_name.endswith( '.zip' ): - new_name = new_name.rstrip( '.zip' ) + # Remove compressed file extensions, if any, but only if + # we're copying files into Galaxy's file space. + if link_data_only == 'copy_files': + if new_name.endswith( '.gz' ): + new_name = new_name.rstrip( '.gz' ) + elif new_name.endswith( '.zip' ): + new_name = new_name.rstrip( '.zip' ) uploaded_dataset.name = new_name uploaded_dataset.path = path uploaded_dataset.type = type @@ -1070,7 +1073,6 @@ if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) - link_data_only = params.get( 'link_data_only', 'copy_files' ) uploaded_dataset.link_data_only = link_data_only if link_data_only == 'link_to_files': uploaded_dataset.data.file_name = os.path.abspath( path ) 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: dan: Add mpileup to tool_conf.xml.main.
by Bitbucket 20 Jan '12

20 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c08d5e96b5dd/ changeset: c08d5e96b5dd user: dan date: 2012-01-20 16:06:24 summary: Add mpileup to tool_conf.xml.main. affected #: 1 file diff -r cb8d6a29ea22612dc575a9f8408af48b46d1a13f -r c08d5e96b5dd8acdc976478cc3cf94b14af501bd tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -380,6 +380,7 @@ <tool file="samtools/sam_to_bam.xml" /><tool file="samtools/bam_to_sam.xml" /><tool file="samtools/sam_merge.xml" /> + <tool file="samtools/samtools_mpileup.xml" /><tool file="samtools/sam_pileup.xml" /><tool file="samtools/pileup_parser.xml" /><tool file="samtools/pileup_interval.xml" /> 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: dan: Add GATK VariantSelect tool.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cb8d6a29ea22/ changeset: cb8d6a29ea22 user: dan date: 2012-01-19 22:16:31 summary: Add GATK VariantSelect tool. affected #: 4 files diff -r 0ebee7a7780521926745c430c94aac081efc6332 -r cb8d6a29ea22612dc575a9f8408af48b46d1a13f test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains --- /dev/null +++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains @@ -0,0 +1,4 @@ +GenomeAnalysisEngine - Strictness is SILENT +SelectVariants - Including sample 'A Fake phiX Sample' +TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining +SelectVariants - 1 records processed. diff -r 0ebee7a7780521926745c430c94aac081efc6332 -r cb8d6a29ea22612dc575a9f8408af48b46d1a13f test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf --- /dev/null +++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf @@ -0,0 +1,31 @@ +##fileformat=VCFv4.1 +##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> +##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> +##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"> +##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes"> +##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> +##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> +##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads"> +##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> +##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> +##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]" +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false" +##contig=<ID=phiX174,length=5386> +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta +##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample +phiX174 1443 . AC . 0 . AC=0;AF=0.00;AN=0;DP=0;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 diff -r 0ebee7a7780521926745c430c94aac081efc6332 -r cb8d6a29ea22612dc575a9f8408af48b46d1a13f tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -403,6 +403,7 @@ <label text="Filtration" id="gatk_filtration" /><tool file="gatk/variant_filtration.xml" /> + <tool file="gatk/variant_select.xml" /><label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /><tool file="gatk/variant_recalibrator.xml" /> diff -r 0ebee7a7780521926745c430c94aac081efc6332 -r cb8d6a29ea22612dc575a9f8408af48b46d1a13f tools/gatk/variant_select.xml --- /dev/null +++ b/tools/gatk/variant_select.xml @@ -0,0 +1,482 @@ +<tool id="gatk_variant_select" name="Select Variants" version="0.0.1"> + <description>from VCF files</description> + <requirements> + <requirement type="package" version="1.3">gatk</requirement> + </requirements> + <command interpreter="python">gatk_wrapper.py + #from binascii import hexlify + --max_jvm_heap_fraction "1" + --stdout "${output_log}" + -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" + -p 'java + -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" + -T "SelectVariants" + --num_threads 4 ##hard coded, for now + -et "NO_ET" ##ET no phone home + -o "${output_vcf}" + + #if $reference_source.reference_source_selector != "history": + -R "${reference_source.ref_file.fields.path}" + #end if + ' + -p ' + #if $input_concordance: + --concordance "${input_concordance}" + #end if + #if $input_discordance: + --discordance "${input_discordance}" + #end if + + #for $exclude_sample_name in $exclude_sample_name_repeat: + --exclude_sample_name "${exclude_sample_name.exclude_sample_name}" + #end for + + ${exclude_filtered} + + #for $sample_name in $sample_name_repeat: + --sample_name "${sample_name.sample_name}" + #end for + + ' + + #for $select_expressions in $select_expressions_repeat: + #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) ) + -o '${ hexlify( $select_expression ) }' + #end for + + ##start tool specific options + #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': + -p ' + #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: + --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" + #end for + + #for $sample_file in $analysis_param_type.sample_file_repeat: + --sample_file "${ample_file.sample_file}" + #end for + + #if $analysis_param_type.input_keep_ids: + --keepIDs "${analysis_param_type.input_keep_ids}" + #end if + + ${analysis_param_type.keep_original_AC} + + ${analysis_param_type.mendelian_violation} + + --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" + + --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}" + + --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}" + + #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction': + --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}" + #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number': + --select_random_number "${analysis_param_type.select_random_type.select_random_number}" + #end if + + #if $analysis_param_type.select_type_to_include: + #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ): + --selectTypeToInclude "${type_to_include}" + #end for + #end if + + ${analysis_param_type.exclude_non_variants} + ' + + #for $sample_expressions in $analysis_param_type.sample_expressions_repeat: + #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) ) + -o '${ hexlify( $sample_expression ) }' + #end for + + #end if + ##end tool specific options + + ##start standard gatk options + #if $gatk_param_type.gatk_param_type_selector == "advanced": + #for $pedigree in $gatk_param_type.pedigree: + -p '--pedigree "${pedigree.pedigree_file}"' + #end for + #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: + -p '--pedigreeString "${pedigree_string.pedigree_string}"' + #end for + -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' + #for $read_filter in $gatk_param_type.read_filter: + -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + ###raise Exception( str( dir( $read_filter ) ) ) + #for $name, $param in $read_filter.read_filter_type.iteritems(): + #if $name not in [ "__current_case__", "read_filter_type_selector" ]: + --${name} "${param}" + #end if + #end for + ' + #end for + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + + -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' + + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' + #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": + -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' + #end if + -p ' + --baq "${gatk_param_type.baq}" + --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}" + ${gatk_param_type.use_original_qualities} + --defaultBaseQualities "${gatk_param_type.default_base_qualities}" + --validation_strictness "${gatk_param_type.validation_strictness}" + --interval_merging "${gatk_param_type.interval_merging}" + ${gatk_param_type.disable_experimental_low_memory_sharding} + ${gatk_param_type.non_deterministic_random_seed} + ' + #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): + #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": + -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for + #end if + + #if str( $reference_source.reference_source_selector ) == "history": + -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" + #end if + ##end standard gatk options + + + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" 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"> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> + <param name="ref_file" type="select" label="Using reference genome"> + <options from_data_table="gatk_picard_indexes"> + <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + + <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data"> + <param name="select_expressions" type="text" label="JEXL expression"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </repeat> + + <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True"/> + <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True"/> + + <repeat name="sample_name_repeat" title="Include Samples by name"> + <param name="sample_name" type="text" label="Include genotypes from this sample"/> + </repeat> + + <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name"> + <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/> + </repeat> + + <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" /> + + <conditional name="gatk_param_type"> + <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> +  + </when> + <when value="advanced"> + <repeat name="pedigree" title="Pedigree file"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + </repeat> + <repeat name="pedigree_string_repeat" title="Pedigree string"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + </repeat> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <option value="STRICT" selected="True">STRICT</option> + <option value="SILENT">SILENT</option> + </param> + <repeat name="read_filter" title="Read Filter"> + <conditional name="read_filter_type"> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> +  + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + </conditional> + </repeat> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + + <param name="interval_set_rule" type="select" label="Interval set rule"> + <option value="UNION" selected="True">UNION</option> + <option value="INTERSECTION">INTERSECTION</option> + </param> + + <conditional name="downsampling_type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="NONE" selected="True">NONE</option> + <option value="ALL_READS">ALL_READS</option> + <option value="BY_SAMPLE">BY_SAMPLE</option> + </param> + <when value="NONE"> +  + </when> + <when value="ALL_READS"> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when> + <when value="BY_SAMPLE"> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when> + </conditional> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <option value="OFF" selected="True">OFF</option> + <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option> + <option value="RECALCULATE">RECALCULATE</option> + </param> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets"/> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <option value="STRICT" selected="True">STRICT</option> + <option value="LENIENT">LENIENT</option> + <option value="SILENT">SILENT</option> +  + </param> + <param name="interval_merging" type="select" label="Interval merging rule"> + <option value="ALL" selected="True">ALL</option> + <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> + </param> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </conditional> + </repeat> + + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality" checked="False"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + + </when> + </conditional> + + + <conditional name="analysis_param_type"> + <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> +  + </when> + <when value="advanced"> + + <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file"> + <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> + </repeat> + + <repeat name="sample_file_repeat" title="Samples by file"> + <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /> + </repeat> + + <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True"/> + + <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" /> + + <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" /> + + <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" /> + + <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" /> + + <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity"> + <option value="ALL" selected="True">ALL</option> + <option value="MULTIALLELIC">MULTIALLELIC</option> + <option value="BIALLELIC">BIALLELIC</option> + </param> + + <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided"> + <param name="sample_expressions" type="text" label="Regular expression"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + </repeat> + + <conditional name="select_random_type"> + <param name="select_random_type_selector" type="select" label="Select a random subset of variants"> + <option value="select_all" selected="True">Use all variants</option> + <option value="select_random_fraction">Select random fraction</option> + <option value="select_random_number">Select random number</option> + </param> + <when value="select_all"> +  + </when> + <when value="select_random_fraction"> + <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1"/> + </when> + <when value="select_random_number"> + <param name="select_random_number" type="integer" value="0" label="Count" /> + </when> + </conditional> + + <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" /> + + <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes"> + <option value="INDEL">INDEL</option> + <option value="SNP">SNP</option> + <option value="MIXED">MIXED</option> + <option value="MNP">MNP</option> + <option value="SYMBOLIC">SYMBOLIC</option> + <option value="NO_VARIATION">NO_VARIATION</option> + </param> + + </when> + </conditional> + + </inputs> + <outputs> + <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> + <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="phiX.fasta" ftype="fasta" /> + <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" /> + <param name="select_expressions_repeat" value="0" /> + <param name="input_concordance" /> + <param name="input_discordance" /> + <param name="exclude_sample_name_repeat" value="0" /> + <param name="exclude_filtered" /> + <param name="sample_name_repeat" value="0" /> + <param name="gatk_param_type_selector" value="basic" /> + <param name="analysis_param_type_selector" value="basic" /> + <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" /> + <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" /> + </test> + </tests> + <help> +**What it does** + +Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the Using JEXL expressions section (http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions) One can optionally include concordance or discordance tracks for use in selecting overlapping variants. + +For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants>`_. + +To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. + +If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. + +------ + +**Inputs** + +GenomeAnalysisTK: SelectVariants accepts a VCF input file. + + +**Outputs** + +The output is in VCF format. + + +Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. + +------- + +**Settings**:: + + + out VCFWriter stdout File to which variants should be written + variant RodBinding[VariantContext] NA Input VCF file + concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track + discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track + exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times + exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times + excludeFiltered boolean false Don't include filtered loci in the analysis + excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure + keepIDs File NA Only emit sites whose ID is found in this file (one ID per line) + keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting + mendelianViolation Boolean false output mendelian violation sites only + mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation + remove_fraction_genotypes double 0.0 Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall + restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC + sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times + sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times + sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times + select_expressions ArrayList[String] [] One or more criteria to use when selecting the data + select_random_fraction double 0.0 Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track + select_random_number int 0 Selects a number of variants at random from the variant track + selectTypeToInclude List[Type] [] Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times + +------ + +**Citation** + +For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </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: greg: Add more flexibility in generating a workflow image in the tool shed.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0ebee7a77805/ changeset: 0ebee7a77805 user: greg date: 2012-01-19 20:58:48 summary: Add more flexibility in generating a workflow image in the tool shed. affected #: 1 file diff -r 5ecec0d061792687699a04543cfe80b7125f54b4 -r 0ebee7a7780521926745c430c94aac081efc6332 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -250,7 +250,22 @@ boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] - out_conn_pos = out_pos[ output_dict[ 'id' ] ][ output_dict[ 'output_name' ] ] + # out_pos_index will be a step number like 1, 2, 3... + out_pos_index = output_dict[ 'id' ] + # out_pos_name will be a string like 'o', 'o2', etc. + out_pos_name = output_dict[ 'output_name' ] + if out_pos_index in out_pos: + # out_conn_index_dict will be something like: + # 7: {'o': (824.5, 618)} + out_conn_index_dict = out_pos[ out_pos_index ] + if out_pos_name in out_conn_index_dict: + out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ] + else: + # Take any key / value pair available in out_conn_index_dict. + # A problem will result if the dictionary is empty. + if out_conn_index_dict.keys(): + key = out_conn_index_dict.keys()[0] + out_conn_pos = out_pos[ out_pos_index ][ key ] adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) text.append( svgfig.SVG( "circle", cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for comparing workflows in repository metadata when resetting all metadata on a tool shed repository.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5ecec0d06179/ changeset: 5ecec0d06179 user: greg date: 2012-01-19 20:23:41 summary: Fix for comparing workflows in repository metadata when resetting all metadata on a tool shed repository. affected #: 1 file diff -r d1e723facfcc043c18f8aa7e9b10797c5f947bdf -r 5ecec0d061792687699a04543cfe80b7125f54b4 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -628,16 +628,20 @@ # Determine if ancestor_workflows is the same as current_workflows # or if ancestor_workflows is a subset of current_workflows. if len( ancestor_workflows ) <= len( current_workflows ): - for ancestor_workflow in ancestor_workflows: + for ancestor_workflow_tup in ancestor_workflows: + # ancestor_workflows is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + ancestor_workflow_dict = ancestor_workflow_tup[1] # Currently the only way to differentiate workflows is by name. - ancestor_workflow_name = ancestor_workflow[ 'name' ] - num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] ) + ancestor_workflow_name = ancestor_workflow_dict[ 'name' ] + num_ancestor_workflow_steps = len( ancestor_workflow_dict[ 'steps' ] ) found_in_current = False - for current_workflow in current_workflows: + for current_workflow_tup in current_workflows: + current_workflow_dict = current_workflow_tup[1] # Assume that if the name and number of steps are euqal, # then the workflows are the same. Of course, this may # not be true... - if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps: + if current_workflow_dict[ 'name' ] == ancestor_workflow_name and len( current_workflow_dict[ 'steps' ] ) == num_ancestor_workflow_steps: found_in_current = True break if not found_in_current: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the drmaa_external_runjob_script attribute to the tool shed's config so that setting repositroy metadata works.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d1e723facfcc/ changeset: d1e723facfcc user: greg date: 2012-01-19 20:21:32 summary: Add the drmaa_external_runjob_script attribute to the tool shed's config so that setting repositroy metadata works. affected #: 1 file diff -r 773fcafde414f13f2d03bc271121c2ccf60db219 -r d1e723facfcc043c18f8aa7e9b10797c5f947bdf lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -87,6 +87,7 @@ # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) + self.drmaa_external_runjob_script = kwargs.get('drmaa_external_runjob_script', None ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add columns for datatypes and workflows in the tool shed repository metadata grid.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/773fcafde414/ changeset: 773fcafde414 user: greg date: 2012-01-19 19:44:00 summary: Add columns for datatypes and workflows in the tool shed repository metadata grid. affected #: 1 file diff -r eb7f68fd5ff1c7703b349be336bdb10945efb32a -r 773fcafde414f13f2d03bc271121c2ccf60db219 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -323,26 +323,41 @@ repo = hg.repository( get_configured_ui(), repository.repo_path ) ctx = get_changectx_for_changeset( trans, repo, repository_metadata.changeset_revision ) return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) - class MetadataColumn( grids.TextColumn ): + class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - metadata_str = '' + tools_str = '' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: - metadata_str += '<b>Tools:</b><br/>' for tool_metadata_dict in metadata[ 'tools' ]: - metadata_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], - tool_metadata_dict[ 'version' ] ) + tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + return tools_str + class DatatypesColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + datatypes_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'datatypes' in metadata: + for datatype_metadata_dict in metadata[ 'datatypes' ]: + datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + return datatypes_str + class WorkflowsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + workflows_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: if 'workflows' in metadata: - metadata_str += '<b>Workflows:</b><br/>' + workflows_str += '<b>Workflows:</b><br/>' # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] workflow_tups = metadata[ 'workflows' ] workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] for workflow_metadata_dict in workflow_metadata_dicts: - metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) - return metadata_str + workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + return workflows_str class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): return repository_metadata.malicious @@ -364,8 +379,12 @@ attach_popup=True ), RevisionColumn( "Revision", attach_popup=False ), - MetadataColumn( "Metadata", - attach_popup=False ), + ToolsColumn( "Tools", + attach_popup=False ), + DatatypesColumn( "Datatypes", + attach_popup=False ), + WorkflowsColumn( "Workflows", + attach_popup=False ), MaliciousColumn( "Malicious", attach_popup=False ) ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for setting tool shed repository metadata.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/921a21a26073/ changeset: 921a21a26073 user: greg date: 2012-01-19 17:03:30 summary: Fix for setting tool shed repository metadata. affected #: 1 file diff -r bebad193a6c498732beac9ecf31b6407f28724fa -r 921a21a2607306f71e6f6775f9256e48ebb0e9ae lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -410,6 +410,8 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + metadata_dict = {} + invalid_files = [] if ctx is not None: if changeset_revision == repository.tip: metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for searching for workflows in the tool shed.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bebad193a6c4/ changeset: bebad193a6c4 user: greg date: 2012-01-19 16:42:39 summary: Fix for searching for workflows in the tool shed. affected #: 2 files diff -r 3b38e670704ff3ce2a3f6b134508a43d008be28c -r bebad193a6c498732beac9ecf31b6407f28724fa lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -336,9 +336,12 @@ tool_metadata_dict[ 'version' ] ) if 'workflows' in metadata: metadata_str += '<b>Workflows:</b><br/>' - for workflow_metadata_dict in metadata[ 'workflows' ]: - metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ], - workflow_metadata_dict[ 'format-version' ] ) + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + workflow_tups = metadata[ 'workflows' ] + workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] + for workflow_metadata_dict in workflow_metadata_dicts: + metadata_str += '%s <b>%s</b><br/>' % ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) return metadata_str class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r 3b38e670704ff3ce2a3f6b134508a43d008be28c -r bebad193a6c498732beac9ecf31b6407f28724fa lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -620,7 +620,10 @@ ok = False elif workflow_names: if 'workflows' in metadata: - workflows = metadata[ 'workflows' ] + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + workflow_tups = metadata[ 'workflows' ] + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] else: workflows = [] for workflow_dict in workflows: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for generating workflow metadata and viewing workflows in tool shed repositories.
by Bitbucket 19 Jan '12

19 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b38e670704f/ changeset: 3b38e670704f user: greg date: 2012-01-19 16:25:28 summary: Fix for generating workflow metadata and viewing workflows in tool shed repositories. affected #: 3 files diff -r ab1a5ab063ce2d5e4e2dfc5759b8714f4f8c2ef3 -r 3b38e670704ff3ce2a3f6b134508a43d008be28c lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -160,7 +160,10 @@ changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata workflow_name = decode( workflow_name ) - for workflow_dict in metadata[ 'workflows' ]: + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + for workflow_tup in metadata[ 'workflows' ]: + workflow_dict = workflow_tup[1] if workflow_dict[ 'name' ] == workflow_name: break if 'tools' in metadata: diff -r ab1a5ab063ce2d5e4e2dfc5759b8714f4f8c2ef3 -r 3b38e670704ff3ce2a3f6b134508a43d008be28c templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -56,6 +56,8 @@ <div style="clear: both"></div> %endif %if 'workflows' in metadata: + ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is + ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] <div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%"> @@ -81,11 +83,8 @@ full_path = os.path.abspath( relative_path ) workflow_dict = workflow_tup[ 1 ] workflow_name = workflow_dict[ 'name' ] - if 'steps' in workflow_dict: - ## Initially steps were not stored in the metadata record. - steps = workflow_dict[ 'steps' ] - else: - steps = [] + ## Initially steps were not stored in the metadata record. + steps = workflow_dict.get( 'steps', [] ) format_version = workflow_dict[ 'format-version' ] annotation = workflow_dict[ 'annotation' ] %> diff -r ab1a5ab063ce2d5e4e2dfc5759b8714f4f8c2ef3 -r 3b38e670704ff3ce2a3f6b134508a43d008be28c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -148,6 +148,8 @@ <div style="clear: both"></div> %endif %if 'workflows' in metadata: + ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is + ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] <div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%"> @@ -157,7 +159,7 @@ </div><div style="clear: both"></div><div class="form-row"> - <% workflow_dicts = metadata[ 'workflows' ] %> + <% workflow_tups = metadata[ 'workflows' ] %><table class="grid"><tr><td><b>name</b></td> @@ -165,14 +167,13 @@ <td><b>format-version</b></td><td><b>annotation</b></td></tr> - %for workflow_dict in workflow_dicts: - <% + %for workflow_tup in workflow_tups: + <% + relative_path = workflow_tup[0] + workflow_dict = workflow_tup[1] workflow_name = workflow_dict[ 'name' ] - if 'steps' in workflow_dict: - ## Initially steps were not stored in the metadata record. - steps = workflow_dict[ 'steps' ] - else: - steps = [] + ## Initially steps were not stored in the metadata record. + steps = workflow_dict.get( 'steps', [] ) format_version = workflow_dict[ 'format-version' ] annotation = workflow_dict[ 'annotation' ] %> 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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