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comparison strelka.xml @ 7:3e8541ece3c7

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trying to fix environment variable 0.0.1
author mini
date Fri, 26 Sep 2014 14:30:27 +0200
parents 87568e5a7d4f
children f66f23fcc83a
comparison
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6:87568e5a7d4f 7:3e8541ece3c7
1 <tool id="strelka88" name="Strelka good interface but no dependencies"> 1 <tool id="strelka88" name="Strelka good interface but no dependencies">
2 2
3 <description>Strelka good interface but no dependencies</description> 3 <description>Strelka good interface but no dependencies</description>
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">SCRIPT_PATH</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 6 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.1.11">vcftools</requirement> 7 <requirement type="package" version="0.1.11">vcftools</requirement>
7 </requirements> 8 </requirements>
8 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile 9 <command interpreter="python">strelka_wrapper.py --tumorBam $tumorBam --normalBam $normalBam --refFile $refFile
9 #if $configuration.configuration_switch == 'Default': 10 #if $configuration.configuration_switch == 'Default':
33 --maxInputDepth $configuration.maxInputDepth 34 --maxInputDepth $configuration.maxInputDepth
34 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes': 35 #if $configuration.extra_arguments.extra_arguments_switch == 'Yes':
35 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments 36 --extraStrelkaArguments $configuration.extra_arguments.extraStrelkaArguments
36 #end if 37 #end if
37 #end if 38 #end if
39 --scriptPath \$SCRIPT_PATH
38 </command> 40 </command>
39 41
40 <inputs> 42 <inputs>
41 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/> 43 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
42 <param format="bam" name="normalBam" type="data" label="Normal bam file"/> 44 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>