1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/5800e807ba4e/ changeset: 5800e807ba4e user: dan date: 2011-10-31 21:20:55 summary: Clean up for some GATK tools. affected #: 4 files

diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r 5800e807ba4e56209e785950d7197bc979d5f244 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -19,8 +19,8 @@ #end if --recal_file "${output_recal}" ${standard_covs} - #if $covariates.value: - #for $cov in $covariates.value: + #if str( $covariates ) != "None": + #for $cov in str( $covariates ).split( ',' ): -cov "${cov}" #end for #end if

diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r 5800e807ba4e56209e785950d7197bc979d5f244 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -112,13 +112,13 @@ --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}" --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" ${analysis_param_type.doContextDependentGapPenalties} - #if $analysis_param_type.annotation.value: - #for $annotation in $analysis_param_type.annotation.value: + #if str( $analysis_param_type.annotation ) != "None": + #for $annotation in str( $analysis_param_type.annotation ).split( ','): --annotation "${annotation}" #end for #end if - #if $analysis_param_type.group.value: - #for $group in $analysis_param_type.group.value: + #if str( $analysis_param_type.group ) != "None": + #for $group in str( $analysis_param_type.group ).split( ','): --group "${group}" #end for #end if

diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r 5800e807ba4e56209e785950d7197bc979d5f244 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -24,7 +24,7 @@ #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations": --useAllAnnotations #else: - #if $annotations_type.annotations.value: + #if str( $annotations_type.annotations ) != "None": #for $annotation in str( $annotations_type.annotations ).split( ',' ): --annotation "${annotation}" #end for @@ -127,7 +127,7 @@ ##end standard gatk options

-p ' - #if $annotation_group.value: + #if str( $annotation_group ) != "None": #for $group in str( $annotation_group ).split( ',' ): --group "${group}" #end for

diff -r 22d844537368bff2acb8eb50bce6561a673002ef -r 5800e807ba4e56209e785950d7197bc979d5f244 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -98,7 +98,7 @@

##start analysis specific options -p ' - #if $annotations.value: + #if str( $annotations ) != "None": #for $annotation in str( $annotations ).split( ',' ): --use_annotation "${annotation}" #end for

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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