Mercurial > repos > yusuf > gvf_to_vcf

diff GVF2VCF.xml @ 0:18d965813efc default tip

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intial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:37:21 -0600
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GVF2VCF.xml	Wed Mar 25 13:37:21 2015 -0600
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+
+<tool id="gvf_to_vcf_1" name="Convert diBayes GVF file to VCF format">
+  <version_string>dibayes_gff2vcf -v</version_string>
+  <command interpreter="perl">dibayes_gff2vcf $input_gff $output_vcf</command>
+  <inputs>
+    <param format="gff3" name="input_gff" type="data" label="GVF file generated by diBayes (may work for other, but untested)"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output_vcf" label="diBayes calls in VCF format"/>
+  </outputs>
+
+  <tests>
+    <test>
+     <param name="input_gff" value="depth_test.bam" ftype="gff"/>
+     <output name="output_vcf">
+       <assert_contents>
+         <has_text text="targeted nucleotide bases: 155091"/>
+         <has_text text="bases mapped to targeted regions: 11473773"/>
+         <has_text text="bases with less than 20-fold coverage: 19046"/>
+       </assert_contents>
+     </output>
+    </test>
+  </tests>
+
+  <help>
+This tool an ABI colorspace sequencing run's variant calls (using LifeScope's diBayes) into a format amenable to many variant processing tools. 
+  </help>
+
+</tool>