<tool id="strelka2" name="Strelka 2" version="1.0.14">
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="0.1.11">vcftools</requirement>
  </requirements>
  <description>Strelka without dependencie built-in</description>
  <command interpreter="python">
   strelka_wrapper.py
    --tumorBam $tumorBam
    --normalBam $normalBam
    --refFile $refFile
    --configFile $configFile
  </command>

  <inputs>
    <param format="bam" name="tumorBam" type="data" label="Tumor bam file"/>
    <param format="bam" name="normalBam" type="data" label="Normal bam file"/>
    <param format="fasta" name="refFile" type="data" label="ref fasta file"/>
    <param format="ini" name="configFile" type="data" label="config file"/>
  </inputs>

  <outputs>
    <data format="vcf" name="output_vcf_1" label="${tool.name} on ${on_string} (passed.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.snvs.vcf" />
    <data format="vcf" name="output_vcf_2" label="${tool.name} on ${on_string} (passed.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/passed.somatic.indels.vcf" />
    <data format="vcf" name="output_vcf_3" label="${tool.name} on ${on_string} (all.somatic.snvs.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.snvs.vcf"  />
    <data format="vcf" name="output_vcf_4" label="${tool.name} on ${on_string} (all.somatic.indels.vcf)" from_work_dir="StrelkaAnalysis/results/all.somatic.indels.vcf"  />
  </outputs>
  <trackster_conf/>


  <help>
Strelka, a method for somatic SNV and small indel detectipon from sequencing data of matched tumor-normal samples.
  </help>

</tool>