Mercurial > repos > jjohnson > defuse8

diff defuse_results_to_vcf.xml @ 0:63f23d5db27c draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 2c2fd38cb761ec57bac7a0bd376e6aa2b88265d0-dirty
author: jjohnson
date: Mon, 20 May 2019 15:25:03 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse_results_to_vcf.xml	Mon May 20 15:25:03 2019 -0400
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<tool id="defuse_results_to_vcf" name="Defuse Results to VCF" version="@DEFUSE_VERSION@.2">
+  <description>generate a VCF from a DeFuse Results file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+  <command detect_errors="default"><![CDATA[
+      $__tool_directory__/defuse_results_to_vcf.py  --input $defuse_results --reference ${defuse_results.metadata.dbkey} --output $vcf
+  ]]></command>
+  <inputs>
+    <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/> 
+  </inputs>
+  <outputs>
+    <data name="vcf" metadata_source="defuse_results" format="vcf"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/>
+      <output name="vcf" file="mm10_results.filtered.vcf"/>
+    </test>
+  </tests>
+  <help>
+**Defuse Results to VCF**
+
+Generates a VCF_ Variant Call Format file from a DeFuse_ results.tsv file.   
+
+This program relies on the header line of the results.tsv to determine which columns to use for genrating the VCF file.   
+
+.. _VCF: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
+.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
+  </help>
+</tool>