diff strelka2/strelka.xml @ 0:7a9f20ca4ad5

Uploaded

--- /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>