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comparison filter.xml @ 1:c559b5bb484b draft

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"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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0:896c846866a6 1:c559b5bb484b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy0" profile="18.01"> 2 <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>somatic or germline structural variants</description> 3 <description>somatic or germline structural variants</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
40 #end if 40 #end if
41 ## samples 41 ## samples
42 'sample.bcf.gz' ## input 42 'sample.bcf.gz' ## input
43 43
44 ## postprocessing 44 ## postprocessing
45 #if 'log' in $oo.out 45 @LOG@
46 |& tee 'log.txt' 46 @VCF@
47 #end if
48 #if 'vcf' in $oo.out
49 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
50 #end if
51 ]]></command> 47 ]]></command>
52 <inputs> 48 <inputs>
53 <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/> 49 <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/>
54 <section name="generic" title="Generic options" expanded="true"> 50 <section name="generic" title="Generic options" expanded="true">
55 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> 51 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
56 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> 52 <expand macro="minsize"/>
57 <param argument="--maxsize" type="integer" value="500000000" label="Set maximum SV size"/> 53 <expand macro="maxsize" default="500000000"/>
58 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> 54 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/>
59 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> 55 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
60 </section> 56 </section>
61 <section name="sv" title="SV calling options" expanded="true"> 57 <section name="sv" title="SV calling options" expanded="true">
62 <conditional name="mode_cond"> 58 <conditional name="mode_cond">