[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.
Bitbucket
commits-noreply at bitbucket.org
Mon Dec 5 12:27:58 EST 2011
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. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the galaxy-commits
mailing list