Mercurial > repos > mini > strelka
comparison strelka.xml @ 7:3e8541ece3c7
trying to fix environment variable 0.0.1
| author | mini |
|---|---|
| date | Fri, 26 Sep 2014 14:30:27 +0200 |
| parents | 87568e5a7d4f |
| children | f66f23fcc83a |
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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"/> |