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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"
author iuc
date Thu, 27 Jan 2022 15:19:23 +0000
parents d262577e04b0
children
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2:d262577e04b0 3:e0734e88a104
2 <description>calls SNVs and indels for tumor-normal pairs</description> 2 <description>calls SNVs and indels for tumor-normal pairs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.10.2">python</requirement>
7 <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
8 <requirement type="package" version="5.1.0">gawk</requirement> 9 <requirement type="package" version="5.1.0">gawk</requirement>
9 <requirement type="package" version="1.14">samtools</requirement> 10 <requirement type="package" version="1.14">samtools</requirement>
10 </requirements> 11 </requirements>
11 <expand macro="stdio" /> 12 <expand macro="stdio" />
30 #if $interval_file: 31 #if $interval_file:
31 grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai && 32 grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
32 #else 33 #else
33 ln -s ./ref.fa.fai ./chromosomes.fa.fai && 34 ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
34 #end if 35 #end if
35 awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed && 36 python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed &&
36 37
37 vardict-java 38 vardict-java
38 #if $select_mode.mode == "paired" 39 #if $select_mode.mode == "paired"
39 -b "./tumor.bam|./normal.bam" 40 -b "./tumor.bam|./normal.bam"
40 -N 'Tumor' 41 -N 'Tumor'
126 </conditional> 127 </conditional>
127 <conditional name="reference_source"> 128 <conditional name="reference_source">
128 <param name="reference_source_selector" value="history"/> 129 <param name="reference_source_selector" value="history"/>
129 <param name="ref_file" ftype="fasta" value="genome.fasta" /> 130 <param name="ref_file" ftype="fasta" value="genome.fasta" />
130 </conditional> 131 </conditional>
132
131 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> 133 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
132 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> 134 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
133 </test> 135 </test>
134 <test expect_num_outputs="2"> 136 <test expect_num_outputs="2">
135 <conditional name="select_mode"> 137 <conditional name="select_mode">
139 </conditional> 141 </conditional>
140 <conditional name="reference_source"> 142 <conditional name="reference_source">
141 <param name="reference_source_selector" value="cached"/> 143 <param name="reference_source_selector" value="cached"/>
142 <param name="ref_file" value="test_buildid"/> 144 <param name="ref_file" value="test_buildid"/>
143 </conditional> 145 </conditional>
146
144 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> 147 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
145 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> 148 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
146 </test> 149 </test>
147 <test expect_num_outputs="2"> 150 <test expect_num_outputs="2">
148 <conditional name="select_mode"> 151 <conditional name="select_mode">