# HG changeset patch
# User jeltje
# Date 1421091746 18000
# Node ID afb57162f9027346ac5ba0261115698565fc2b44
# Parent  41c4eb01c566a0d658a4ecde705080763080d0ae
Uploaded

diff -r 41c4eb01c566 -r afb57162f902 samtools_mpileup.xml
--- a/samtools_mpileup.xml	Mon Jan 12 14:31:17 2015 -0500
+++ b/samtools_mpileup.xml	Mon Jan 12 14:42:26 2015 -0500
@@ -3,13 +3,18 @@
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description>runs basic mpileup on input control and tumor files</description>
+  <command>samtools mpileup "$bamc" "$bamt"> "$output1"
+<!--
   <command>samtools mpileup -q 1 -B "$index" "$bamc" "$bamt"> "$output1"
+-->
   </command>
   <inputs>
     <param name="bamc" type="data" format="bam" label="BAM file (control)" />
     <param name="bamt" type="data" format="bam" label="BAM file (tumor)" />
+<!--
     <param name="index" type="select">
     <options from_data_table="picard_index" />
+-->
   </param>
   </inputs>
   <outputs>