Mercurial > repos > artbio > lumpy_smoove

comparison vcf2hrdetect.xml @ 8:b4dec06d8fc6 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
author artbio
date Sun, 09 May 2021 17:09:33 +0000
parents ad8853ee9909
children 7dcf61950215
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7:8b0005fdfd04 8:b4dec06d8fc6
1 <tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> 1 <tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="2">
2 <description>to tabular hrdetect</description> 2 <description>to tabular hrdetect</description>
3 <requirements>
4 <requirement type="package" version="0.2.5">smoove</requirement>
5 </requirements>
3 <macros> 6 <macros>
4 <import>macro_lumpy_smoove.xml</import> 7 <import>macro_lumpy_smoove.xml</import>
5 </macros> 8 </macros>
6 <stdio> 9 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 10 <exit_code range="1:" level="fatal" description="Tool exception" />
19 </outputs> 22 </outputs>
20 23
21 <tests> 24 <tests>
22 <test> 25 <test>
23 <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> 26 <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" />
24 <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> 27 <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" sort="true" ftype="tabular" />
25 </test> 28 </test>
26 </tests> 29 </tests>
27 <help> 30 <help>
28 **vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with 31 **vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with
29 the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv) 32 the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv)