Mercurial > repos > iuc > delly_filter
comparison filter.xml @ 1:9919057a466c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author | iuc |
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date | Thu, 29 Oct 2020 20:50:57 +0000 |
parents | a75e05f20a66 |
children | 6184cfc70e28 |
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0:a75e05f20a66 | 1:9919057a466c |
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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"> |