1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/35be930b21be/ changeset: 35be930b21be user: dan date: 2012-03-01 16:11:55 summary: Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined. affected #: 1 file diff -r 49f8ed2c6109024446b30e9110aea274e60378c3 -r 35be930b21bea104bd574d4e9854c6e9c1a58cdb tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -129,7 +129,7 @@ && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} #end if @@ -148,7 +148,7 @@ && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} #end if @@ -167,7 +167,7 @@ && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} #end if 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.