Mercurial > repos > artbio > lumpy_smoove
view vcf2hrdetect.xml @ 6:ad8853ee9909 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
author | artbio |
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date | Sun, 14 Feb 2021 23:59:42 +0000 |
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children | b4dec06d8fc6 |
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<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> <description>to tabular hrdetect</description> <macros> <import>macro_lumpy_smoove.xml</import> </macros> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ @pipefail@ python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular' ]]></command> <inputs> <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/> </inputs> <outputs> <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" /> </outputs> <tests> <test> <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> </test> </tests> <help> **vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv) </help> <citations> <citation type="doi">10.1038/nm.4292</citation> </citations> </tool>