Mercurial > repos > iuc > vardict_java

comparison vardict.xml @ 2:d262577e04b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e"
author iuc
date Tue, 16 Nov 2021 19:05:56 +0000
parents 5f756651a1bc
children e0734e88a104
comparison
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1:5f756651a1bc 2:d262577e04b0
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="@TOOL_VERSION@">vardict-java</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
8 <requirement type="package" version="5.0.1">gawk</requirement> 8 <requirement type="package" version="5.1.0">gawk</requirement>
9 <requirement type="package" version="1.10">samtools</requirement> 9 <requirement type="package" version="1.14">samtools</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #if $select_mode.mode == "paired" 13 #if $select_mode.mode == "paired"
14 ln -s '$select_mode.normal' ./normal.bam && 14 ln -s '$select_mode.normal' ./normal.bam &&
84 ]]></command> 84 ]]></command>
85 <inputs> 85 <inputs>
86 <conditional name="select_mode"> 86 <conditional name="select_mode">
87 <param name="mode" type="select" label="Choose run mode"> 87 <param name="mode" type="select" label="Choose run mode">
88 <option value="single">Single sample mode</option> 88 <option value="single">Single sample mode</option>
89 <option value="paired" selected="True">Paired variant calling</option> 89 <option value="paired" selected="true">Paired variant calling</option>
90 </param> 90 </param>
91 <when value="single"> 91 <when value="single">
92 <expand macro="input_default" /> 92 <expand macro="input_default" />
93 </when> 93 </when>
94 <when value="paired"> 94 <when value="paired">
95 <param name="normal" type="data" format="bam" label="Normal file" /> 95 <param name="normal" type="data" format="bam" label="Normal file" />
96 <expand macro="input_default" /> 96 <expand macro="input_default" />
97 </when> 97 </when>
98 </conditional> 98 </conditional>
99 <section name="advancedsettings" title="Advanced Settings" expanded="False"> 99 <section name="advancedsettings" title="Advanced Settings" expanded="false">
100 <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" /> 100 <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" />
101 <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" /> 101 <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" />
102 <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" /> 102 <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" />
103 <param argument="-B" type="integer" min="0" value="2" label="Minimum number of reads for determining strand bias" /> 103 <param argument="-B" type="integer" min="0" value="2" label="Minimum number of reads for determining strand bias" />
104 <param argument="-Q" type="integer" min="0" value="1" label="Minimum mapping quality for reads to be considered" /> 104 <param argument="-Q" type="integer" min="0" value="1" label="Minimum mapping quality for reads to be considered" />
126 </conditional> 126 </conditional>
127 <conditional name="reference_source"> 127 <conditional name="reference_source">
128 <param name="reference_source_selector" value="history"/> 128 <param name="reference_source_selector" value="history"/>
129 <param name="ref_file" ftype="fasta" value="genome.fasta" /> 129 <param name="ref_file" ftype="fasta" value="genome.fasta" />
130 </conditional> 130 </conditional>
131 <output name="all_variants" file="all_variants_paired.vcf" /> 131 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
132 <output name="passed_variants" file="passed_variants_paired.vcf" /> 132 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
133 </test> 133 </test>
134 <test expect_num_outputs="2"> 134 <test expect_num_outputs="2">
135 <conditional name="select_mode"> 135 <conditional name="select_mode">
136 <param name="mode" value="paired" /> 136 <param name="mode" value="paired" />
137 <param name="normal" ftype="bam" value="normal.bam" /> 137 <param name="normal" ftype="bam" value="normal.bam" />
139 </conditional> 139 </conditional>
140 <conditional name="reference_source"> 140 <conditional name="reference_source">
141 <param name="reference_source_selector" value="cached"/> 141 <param name="reference_source_selector" value="cached"/>
142 <param name="ref_file" value="test_buildid"/> 142 <param name="ref_file" value="test_buildid"/>
143 </conditional> 143 </conditional>
144 <output name="all_variants" file="all_variants_paired.vcf" /> 144 <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
145 <output name="passed_variants" file="passed_variants_paired.vcf" /> 145 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
146 </test> 146 </test>
147 <test expect_num_outputs="2"> 147 <test expect_num_outputs="2">
148 <conditional name="select_mode"> 148 <conditional name="select_mode">
149 <param name="mode" value="single" /> 149 <param name="mode" value="single" />
150 <param name="tumor" ftype="bam" value="tumor.bam" /> 150 <param name="tumor" ftype="bam" value="tumor.bam" />
151 </conditional> 151 </conditional>
152 <conditional name="reference_source"> 152 <conditional name="reference_source">
153 <param name="reference_source_selector" value="cached"/> 153 <param name="reference_source_selector" value="cached"/>
154 <param name="ref_file" value="test_buildid"/> 154 <param name="ref_file" value="test_buildid"/>
155 </conditional> 155 </conditional>
156 <output name="all_variants" file="all_variants_single.vcf" /> 156 <output name="all_variants" compare="re_match_multiline" file="all_variants_single.vcf" />
157 <output name="passed_variants" file="passed_variants_single.vcf" /> 157 <output name="passed_variants" compare="re_match_multiline" file="passed_variants_single.vcf" />
158 </test> 158 </test>
159 </tests> 159 </tests>
160 <help> 160 <help>
161 <![CDATA[ 161 <![CDATA[
162 VarDict 162 VarDict