1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0a901d00d880/ changeset: 0a901d00d880 user: dan date: 2011-12-06 15:42:56 summary: Update GATK tools handling annotations to allow manually specifying additional annotation names to apply. affected #: 3 files
diff -r bbda064ee4b6ffff2d867a389b81d884c772aa12 -r 0a901d00d8807a50017840e72fa37f2bf7cf2bcf tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -117,6 +117,9 @@ --annotation "${annotation}" #end for #end if + #for $additional_annotation in $analysis_param_type.additional_annotations: + --annotation "${additional_annotation.additional_annotation_name}" + #end for #if str( $analysis_param_type.group ) != "None": #for $group in str( $analysis_param_type.group ).split( ','): --group "${group}" @@ -372,6 +375,9 @@ <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options></param> + <repeat name="additional_annotations" title="Additional annotation"> + <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> + </repeat><!-- <conditional name="snpEff_rod_bind_type"><param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
diff -r bbda064ee4b6ffff2d867a389b81d884c772aa12 -r 0a901d00d8807a50017840e72fa37f2bf7cf2bcf tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -36,14 +36,9 @@ --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(): -## #if $name not in [ "__current_case__", "additional_annotation_type_selector" ]: -## --${name} "${param}" -## #end if -## #end for -## #end for + #for $additional_annotation in $additional_annotations: + --annotation "${additional_annotation.additional_annotation_name}" + #end for ${reference_source.input_variant_bti} '
@@ -188,6 +183,10 @@ </when></conditional>
+ <repeat name="additional_annotations" title="Additional annotation"> + <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> + </repeat> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"><param name="comp_input_rod" type="data" format="vcf" label="ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
diff -r bbda064ee4b6ffff2d867a389b81d884c772aa12 -r 0a901d00d8807a50017840e72fa37f2bf7cf2bcf tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -104,6 +104,9 @@ --use_annotation "${annotation}" #end for #end if + #for $additional_annotation in $additional_annotations: + --use_annotation "${additional_annotation.additional_annotation_name}" + #end for --mode "${mode}" '
@@ -344,11 +347,15 @@ </options></param>
- <param name="mode" type="select" label="Recalibration mode"> - <option value="SNP" selected="True">SNP</option> - <option value="INDEL">INDEL</option> - <option value="BOTH">BOTH</option> - </param> + <repeat name="additional_annotations" title="Additional annotation"> + <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> + </repeat> + + <param name="mode" type="select" label="Recalibration mode"> + <option value="SNP" selected="True">SNP</option> + <option value="INDEL">INDEL</option> + <option value="BOTH">BOTH</option> + </param><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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