Mercurial > repos > mini > strelka
diff strelka2/strelka.xml @ 0:7a9f20ca4ad5
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author | mini |
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date | Thu, 25 Sep 2014 11:59:08 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/strelka2/strelka.xml Thu Sep 25 11:59:08 2014 -0400 @@ -0,0 +1,35 @@ +<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>