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comparison strelka2/strelka.xml @ 0:7a9f20ca4ad5

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author mini
date Thu, 25 Sep 2014 11:59:08 -0400
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1 <tool id="strelka2" name="Strelka 2" version="1.0.14">
2 <requirements>
3 <requirement type="package" version="0.1.18">samtools</requirement>
4 <requirement type="package" version="0.1.11">vcftools</requirement>
5 </requirements>
6 <description>Strelka without dependencie built-in</description>
7 <command interpreter="python">
8 strelka_wrapper.py
9 --tumorBam $tumorBam
10 --normalBam $normalBam
11 --refFile $refFile
12 --configFile $configFile
13 </command>
14
15 <inputs>
16 <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
17 <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
18 <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
19 <param format="ini" name="configFile" type="data" label="config file"/>
20 </inputs>
21
22 <outputs>
23 <data format="vcf" name="output_vcf_1" label="${tool.name} on ${on_string} (passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf" />
24 <data format="vcf" name="output_vcf_2" label="${tool.name} on ${on_string} (passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf" />
25 <data format="vcf" name="output_vcf_3" label="${tool.name} on ${on_string} (all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf" />
26 <data format="vcf" name="output_vcf_4" label="${tool.name} on ${on_string} (all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf" />
27 </outputs>
28 <trackster_conf/>
29
30
31 <help>
32 Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
33 </help>
34
35 </tool>