commit/galaxy-central: dan: Updates for GATK tools.

29 Nov 2011

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)" />

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