[galaxy-commits] commit/galaxy-central: dan: GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/46e455a590e5/ changeset: 46e455a590e5 user: dan date: 2011-12-05 18:27:54 summary: GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file. affected #: 5 files diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tool-data/gatk_annotations.txt.sample --- /dev/null +++ b/tool-data/gatk_annotations.txt.sample @@ -0,0 +1,30 @@ +#unique_id name gatk_value tools_valid_for +AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +DepthOfCoverage DepthOfCoverage DepthOfCoverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +IndelType IndelType IndelType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +MappingQualityZeroFraction MappingQualityZeroFraction MappingQualityZeroFraction UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator +SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator +TechnologyComposition TechnologyComposition TechnologyComposition UnifiedGenotyper,VariantAnnotator,VariantRecalibrator diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tool-data/gatk_sorted_picard_index.loc.sample --- /dev/null +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Picard dict and associated files. You will need +#to create these data files and then create a picard_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The picard_index.loc +#file has this format (longer white space is the TAB character): +# +#<unique_build_id><dbkey><display_name><fasta_file_path> +# +#So, for example, if you had hg18 indexed and stored in +#/depot/data2/galaxy/srma/hg18/, +#then the srma_index.loc entry would look like this: +# +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +# +#and your /depot/data2/galaxy/srma/hg18/ directory +#would contain the following three files: +#hg18.fa +#hg18.dict +#hg18.fa.fai +# +#The dictionary file for each reference (ex. hg18.dict) must be +#created via Picard (http://picard.sourceforge.net). Note that +#the dict file does not have the .fa extension although the +#path list in the loc file does include it. +# diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -113,7 +113,7 @@ --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" ${analysis_param_type.doContextDependentGapPenalties} #if str( $analysis_param_type.annotation ) != "None": - #for $annotation in str( $analysis_param_type.annotation ).split( ','): + #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): --annotation "${annotation}" #end for #end if @@ -123,7 +123,7 @@ #end for #end if #if str( $analysis_param_type.exclude_annotations ) != "None": - #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','): + #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): --excludeAnnotation "${annotation}" #end for #end if @@ -366,35 +366,11 @@ <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="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" /> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options></param><!-- <conditional name="snpEff_rod_bind_type"> @@ -420,36 +396,11 @@ </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" /> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> + </options></param></when></conditional> diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -26,13 +26,13 @@ --useAllAnnotations #else: #if str( $annotations_type.annotations ) != "None": - #for $annotation in str( $annotations_type.annotations ).split( ',' ): + #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ): --annotation "${annotation}" #end for #end if #end if #if str( $exclude_annotations ) != "None": - #for $annotation in str( $exclude_annotations ).split( ',' ): + #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ): --excludeAnnotation "${annotation}" #end for #end if @@ -179,36 +179,11 @@ </when><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="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" /> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + </options></param></when></conditional> @@ -388,36 +363,11 @@ <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" /> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/> + </options></param></inputs> diff -r 943855e11c853ec7c8ab7a64ee07a65daefe4374 -r 46e455a590e5923db81cda0034d6192503ce29a6 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -100,7 +100,7 @@ ##start analysis specific options -p ' #if str( $annotations ) != "None": - #for $annotation in str( $annotations ).split( ',' ): + #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): --use_annotation "${annotation}" #end for #end if @@ -337,36 +337,11 @@ </repeat><param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations"> - <!-- 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"/> + <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> + <options from_data_table="gatk_annotations"> + <filter type="multiple_splitter" column="tools_valid_for" separator=","/> + <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> + </options></param><param name="mode" type="select" label="Recalibration mode"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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