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1 <tool id="strelka2" name="Strelka 2" version="1.0.14">
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2 <requirements>
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3 <requirement type="package" version="0.1.18">samtools</requirement>
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4 <requirement type="package" version="0.1.11">vcftools</requirement>
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5 </requirements>
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6 <description>Strelka without dependencie built-in</description>
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7 <command interpreter="python">
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8 strelka_wrapper.py
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9 --tumorBam $tumorBam
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10 --normalBam $normalBam
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11 --refFile $refFile
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12 --configFile $configFile
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13 </command>
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14
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15 <inputs>
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16 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
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17 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
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18 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
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19 <param format="ini" name="configFile" type="data" label="config file"/>
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20 </inputs>
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21
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22 <outputs>
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23 <data format="vcf" name="output_vcf_1" label="${tool.name} on ${on_string} (passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf" />
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24 <data format="vcf" name="output_vcf_2" label="${tool.name} on ${on_string} (passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf" />
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25 <data format="vcf" name="output_vcf_3" label="${tool.name} on ${on_string} (all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf" />
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26 <data format="vcf" name="output_vcf_4" label="${tool.name} on ${on_string} (all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf" />
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27 </outputs>
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28 <trackster_conf/>
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29
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30
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31 <help>
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32 Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
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33 </help>
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34
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35 </tool>
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