# HG changeset patch
# User jeltje
# Date 1421092337 18000
# Node ID ab1f85b31fe9d8e502173eb1922f73db65221f77
# Parent  117867d6f99e85f1138ef2075fb4eac1ccb4c804
Uploaded

diff -r 117867d6f99e -r ab1f85b31fe9 samtools_flagstat.xml
--- a/samtools_flagstat.xml	Mon Jan 12 14:50:13 2015 -0500
+++ b/samtools_flagstat.xml	Mon Jan 12 14:52:17 2015 -0500
@@ -2,11 +2,12 @@
   <requirements>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
-  <description>provides simple stats on BAM files</description>
-  <command>samtools flagstat "$input1" > "$output1"
+  <description>creates mpileup for VarScan2</description>
+  <command>samtools flagstat "$input1" "$input2" > "$output1"
   </command>
   <inputs>
     <param name="input1" type="data" format="bam" label="BAM File" />
+    <param name="input2" type="data" format="bam" label="BAM File" />
   </inputs>
   <outputs>
     <data name="output1" format="txt" />