Mercurial > repos > iuc > delly_filter
diff filter.xml @ 1:c559b5bb484b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
| author | iuc |
|---|---|
| date | Thu, 29 Oct 2020 20:48:16 +0000 |
| parents | 896c846866a6 |
| children | 445e356988a7 |
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--- a/filter.xml Mon Sep 28 07:42:16 2020 +0000 +++ b/filter.xml Thu Oct 29 20:48:16 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01"> +<tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> <description>somatic or germline structural variants</description> <macros> <import>macros.xml</import> @@ -42,19 +42,15 @@ 'sample.bcf.gz' ## input ## postprocessing -#if 'log' in $oo.out - |& tee 'log.txt' -#end if -#if 'vcf' in $oo.out - && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' -#end if +@LOG@ +@VCF@ ]]></command> <inputs> <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/> <section name="generic" title="Generic options" expanded="true"> <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> - <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> - <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/> + <expand macro="minsize"/> + <expand macro="maxsize" default="500000000"/> <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> </section>