1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/19c4b36d6981/ changeset: 19c4b36d6981 user: dan date: 2012-02-02 17:05:05 summary: FreeBayes: make trace and failed alleles outputs optional. affected #: 1 file

diff -r 50bf77aa34c3689a122187d7ba9b55deb348df92 -r 19c4b36d6981ab6d938167a7a6237f41425d6cb5 tools/variant_detection/freebayes.xml --- a/tools/variant_detection/freebayes.xml +++ b/tools/variant_detection/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.1"> +<tool id="freebayes" name="FreeBayes" version="0.0.2"><requirements><requirement type="package" version="0.9.4">freebayes</requirement><requirement type="package">samtools</requirement> @@ -29,11 +29,17 @@

##outputs --vcf "${output_vcf}" - --trace "${output_trace}" - --failed-alleles "${output_failed_alleles_bed}"

##advanced options #if str( $options_type.options_type_selector ) == "advanced": + #additional outputs + #if $options_type.output_trace_option: + --trace "${output_trace}" + #end if + #if $options_type.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + ##additional inputs #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file": --targets "${options_type.target_limit_type.input_target_bed}" @@ -186,8 +192,13 @@ <!-- Do nothing here --></when><when value="advanced"> - - <!-- input and output --> + + <!-- output --> + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" /> + + + <!-- input --><conditional name="target_limit_type"><param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"><option value="do_not_limit" selected="True">Do not limit</option> @@ -398,8 +409,12 @@ </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> - <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)" /> - <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)" /> + <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter> + </data> + <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)"> + <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter> + </data></outputs><tests><test> @@ -408,8 +423,8 @@ <param name="input_bam" ftype="bam" value="gatk/fake_phiX_reads_1.bam"/><param name="options_type_selector" value="basic"/><output name="output_vcf" file="variant_detection/freebayes/freebayes_out_1.vcf.contains" compare="contains"/> - <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> - <output name="output_failed_alleles_bed" file="empty_file.dat" /> + <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" /> + <output name="output_trace" file="variant_detection/freebayes/freebayes_out_1.output_trace" /> --></test></tests><help>

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