# HG changeset patch
# User jingchunzhu
# Date 1439527682 25200
# Node ID e2627dcbd8b9fd431b544e1c552632b324b32966
# Parent  bb8963939d6f815b99ade191a78120b40f6b2f9b
start vcfToXena

diff -r bb8963939d6f -r e2627dcbd8b9 vcfToXena.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfToXena.xml	Thu Aug 13 21:48:02 2015 -0700
@@ -0,0 +1,22 @@
+<tool id="vcfToXena" name="vcfToXena" version="0.1">
+    <description>Vcf To Xena positional mutation data</description>
+    <command>
+      java -Xmx4G -jar $__tool_directory__/snpEff/snpEff.jar  -c $__tool_directory__/snpEff/snpEff.config 
+      -i vcf -upDownStreamLen 5000 $genome
+      $input > $snpeff_output 
+    </command>
+    <inputs>
+        <param format="vcf" name="input" type="data" label="Input VCF file"/>
+	<param name="genome" type="select" label="Genome">
+	  <option value="hg19">hg19</option>
+	</param>
+
+    </inputs>
+    <outputs>
+        <data format="vcf" name="snpeff_output" />
+    </outputs>
+    <help>
+      This tool convert vcf files to xena ready positional mutation data files.
+    </help>
+</tool>
+