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comparison merge.xml @ 1:97c7441aed0d 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 20:51:37 +0000
parents 6331d804f983
children 148389992630
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0:6331d804f983 1:97c7441aed0d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy0" profile="18.01"> 2 <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>structural variants across/within VCF/BCF file(s)</description> 3 <description>structural variants across/within VCF/BCF file(s)</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"/>
36 #for $i, $current in enumerate($samples) 36 #for $i, $current in enumerate($samples)
37 'sample_${i}.bcf.gz' 37 'sample_${i}.bcf.gz'
38 #end for 38 #end for
39 39
40 ## postprocessing 40 ## postprocessing
41 #if 'log' in $oo.out 41 @LOG@
42 |& tee 'log.txt' 42 @VCF@
43 #end if
44 #if 'vcf' in $oo.out
45 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
46 #end if
47 ]]></command> 43 ]]></command>
48 <inputs> 44 <inputs>
49 <expand macro="samples" format="bcf,vcf"/> 45 <expand macro="samples" format="bcf,vcf"/>
50 <section name="generic" title="Generic options" expanded="true"> 46 <section name="generic" title="Generic options" expanded="true">
51 <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/> 47 <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/>
52 <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> 48 <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
53 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/> 49 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/>
54 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> 50 <expand macro="minsize"/>
55 <param argument="--maxsize" type="integer" value="1000000" label="Set maximum SV size"/> 51 <expand macro="maxsize"/>
56 <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/> 52 <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/>
57 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> 53 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
58 </section> 54 </section>
59 <section name="overlap" title="Overlap options" expanded="true"> 55 <section name="overlap" title="Overlap options" expanded="true">
60 <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/> 56 <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/>