Mercurial > repos > artbio > lumpy_smoove

comparison lumpy_smoove.xml @ 7:8b0005fdfd04 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 558dc75a7a265e2b3572d9ce938d9f9f5673abda"
author artbio
date Sun, 18 Apr 2021 17:08:22 +0000
parents ad8853ee9909
children b4dec06d8fc6
comparison
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6:ad8853ee9909 7:8b0005fdfd04
1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy6"> 1 <tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.5+galaxy7">
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>
23 #else: 23 #else:
24 #for $sample in $set_plan.cohort: 24 #for $sample in $set_plan.cohort:
25 ln -s $sample ${sample.element_identifier}.bam && 25 ln -s $sample ${sample.element_identifier}.bam &&
26 ln -f -s $sample.metadata.bam_index ${sample.element_identifier}.bam.bai && 26 ln -f -s $sample.metadata.bam_index ${sample.element_identifier}.bam.bai &&
27 #end for 27 #end for
28 ls -la &&
29 #end if 28 #end if
30 29
31 smoove call --name output 30 smoove call --name output
32 #if $set_exclusion.choices=="yes": 31 #if $set_exclusion.choices=="yes":
33 --exclude $bedmask 32 --exclude $bedmask
37 --genotype 36 --genotype
38 #if $prpos=="no": 37 #if $prpos=="no":
39 --removepr 38 --removepr
40 #end if 39 #end if
41 *.bam && 40 *.bam &&
42 ls -latr && 41 gunzip -c output-smoove.genotyped.vcf.gz > $vcf_call
43 gunzip output-smoove.genotyped.vcf.gz
44 42
45 ]]></command> 43 ]]></command>
46 <inputs> 44 <inputs>
47 <expand macro="reference_source_conditional" /> 45 <expand macro="reference_source_conditional" />
48 <conditional name="set_plan"> 46 <conditional name="set_plan">
80 <option value="yes">Yes</option> 78 <option value="yes">Yes</option>
81 </param> 79 </param>
82 </inputs> 80 </inputs>
83 81
84 <outputs> 82 <outputs>
85 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" from_work_dir="./output-smoove.genotyped.vcf" /> 83 <data format="vcf" name="vcf_call" label="lumpy-smoove Variant Calling" />
86 </outputs> 84 </outputs>
87 85
88 <tests> 86 <tests>
89 <test> 87 <test>
90 88