# HG changeset patch
# User jeltje
# Date 1421092465 18000
# Node ID 6757453c6af9e0d296a41f5b739f20992732c869
# Parent  ab1f85b31fe9d8e502173eb1922f73db65221f77
Uploaded

diff -r ab1f85b31fe9 -r 6757453c6af9 samtools_flagstat.xml
--- a/samtools_flagstat.xml	Mon Jan 12 14:52:17 2015 -0500
+++ b/samtools_flagstat.xml	Mon Jan 12 14:54:25 2015 -0500
@@ -3,7 +3,7 @@
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description>creates mpileup for VarScan2</description>
-  <command>samtools flagstat "$input1" "$input2" > "$output1"
+  <command>samtools mpileup "$input1" "$input2" > "$output1"
   </command>
   <inputs>
     <param name="input1" type="data" format="bam" label="BAM File" />
@@ -22,7 +22,8 @@
 -->
   <help>
 
-This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file.
+This tool runs the mpileup command of samtools 0.1.18
+with flags -q 1 -B
 
   </help>
 </tool>