Mercurial > repos > artbio > lumpy_smoove
comparison vcf2hrdetect.xml @ 6:ad8853ee9909 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 7d69f5c91e7ec5e252e9728fdfb0f7bcc254bf24"
| author | artbio |
|---|---|
| date | Sun, 14 Feb 2021 23:59:42 +0000 |
| parents | |
| children | b4dec06d8fc6 |
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| 5:bd4135caa3fa | 6:ad8853ee9909 |
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| 1 <tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1"> | |
| 2 <description>to tabular hrdetect</description> | |
| 3 <macros> | |
| 4 <import>macro_lumpy_smoove.xml</import> | |
| 5 </macros> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 8 </stdio> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 @pipefail@ | |
| 11 python '$__tool_directory__'/vcf2hrdetect.py '$lumpy_smoove_vcf' '$hrdetect_tabular' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param name="lumpy_smoove_vcf" type="data" format="vcf" label="lumpy-smoove vcf to process"/> | |
| 15 </inputs> | |
| 16 | |
| 17 <outputs> | |
| 18 <data format="tabular" name="hrdetect_tabular" label="tabular hrdetec SVs" /> | |
| 19 </outputs> | |
| 20 | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" /> | |
| 24 <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 **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) | |
| 30 </help> | |
| 31 | |
| 32 <citations> | |
| 33 <citation type="doi">10.1038/nm.4292</citation> | |
| 34 </citations> | |
| 35 </tool> |