Mercurial > repos > artbio > lumpy_smoove

comparison lumpy_smoove.xml @ 2:49a8a327cc72 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"
author artbio
date Wed, 26 Aug 2020 05:48:01 -0400
parents ee8fc44b1655
children 65b400409455
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1:41e68da5c0fe 2:49a8a327cc72
1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.0"> 1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.4.0">
2 <description>find structural variants using the smoove workflow</description> 2 <description>find structural variants using the smoove workflow</description>
3 <macros> 3 <macros>
4 <import>macro_lumpy_smoove.xml</import> 4 <import>macro_lumpy_smoove.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
17 17
18 smoove call -x --name output 18 smoove call -x --name output
19 #if $set_exclusion.choices=="yes": 19 #if $set_exclusion.choices=="yes":
20 --exclude $bedmask 20 --exclude $bedmask
21 #end if 21 #end if
22 --fasta reference.fa -p 24 normal.bam tumor.bam && 22 --fasta reference.fa -p \${GALAXY_SLOTS:-4} normal.bam tumor.bam &&
23 gunzip output-smoove.vcf.gz 23 gunzip output-smoove.vcf.gz
24 #if $prpos=="no": 24 #if $prpos=="no":
25 && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf 25 && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf
26 #end if 26 #end if
27 27