1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9ee4e2e41fd6/ changeset: 9ee4e2e41fd6 user: dan date: 2011-11-29 22:45:37 summary: Updates for GATK tools. affected #: 2 files
diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -1,4 +1,4 @@ -<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4"> +<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.5"><description>SNP and indel caller</description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -122,7 +122,18 @@ --group "${group}" #end for #end if + #if str( $analysis_param_type.exclude_annotations ) != "None": + #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','): + --excludeAnnotation "${annotation}" + #end for + #end if ' +## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': +## -p '--annotation "SnpEff"' +## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}" +## #else: +## -p '--excludeAnnotation "SnpEff"' +## #end if #end if </command><inputs> @@ -354,42 +365,91 @@ <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /><param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <!-- <option value="SnpEff" /> --> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param> +<!-- + <conditional name="snpEff_rod_bind_type"> + <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> + <option value="set_snpEff">Set snpEff</option> + <option value="exclude_snpEff" selected="True">Don't set snpEff</option> + </param> + <when value="exclude_snpEff"> + </when> + <when value="set_snpEff"> + <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> + <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> + </when> + </conditional> +--><param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> - <option value="Standard">Standard</option> - <option value="Experimental">Experimental</option> - <option value="WorkInProgress">WorkInProgress</option> - <!-- <option value="none">none</option> --> + <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> + <option value="Standard">Standard</option> + <option value="Experimental">Experimental</option> + <option value="WorkInProgress">WorkInProgress</option> + <option value="RankSumTest">RankSumTest</option> + <!-- <option value="none">none</option> --></param> + <!-- <param name="family_string" type="text" value="" label="Family String"/> --> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > + <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? --> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <!-- <option value="SnpEff" /> --> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param></when></conditional></inputs>
diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3"> +<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.4"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -13,6 +13,7 @@ -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" + ##--list -T "VariantAnnotator" ##--num_threads 4 ##hard coded, for now -et "NO_ET" ##ET no phone home @@ -30,6 +31,11 @@ #end for #end if #end if + #if str( $exclude_annotations ) != "None": + #for $annotation in str( $exclude_annotations ).split( ',' ): + --excludeAnnotation "${annotation}" + #end for + #end if ## #for $additional_annotation in $additional_annotations: ## --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}" ## #for $name, $param in $additional_annotation.additional_annotation_type.iteritems(): @@ -55,7 +61,10 @@ #end for
#if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': - -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + -p '--annotation "SnpEff"' + -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + #else: + -p '--excludeAnnotation "SnpEff"' #end if
#for $expression in $expressions: @@ -124,6 +133,10 @@ --group "${group}" #end for #end if + #if str( $family_string ) != "": + --family_string "${family_string}" + #end if + --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}" ' </command><inputs> @@ -166,35 +179,35 @@ <when value="choose"><param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" ><!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? --> - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param></when></conditional> @@ -371,7 +384,41 @@ <option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option></param> - + <param name="family_string" type="text" value="" label="Family String"/> + <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > + <!-- might we want to load the available annotations from an external configuration file, since additional ones can be added to local installs? --> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param> + </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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