# HG changeset patch
# User soh.ishiguro3914@gmail.com
# Date 1416560682 -32400
# Node ID 7a9c736bc13c45951c5adb22cd338af6151a231c
# Parent  2d4f69268768b3204e0c577d97983411af5b6a74
Add flagstat

diff -r 2d4f69268768 -r 7a9c736bc13c samtools_v1_1.xml
--- a/samtools_v1_1.xml	Fri Nov 21 17:56:10 2014 +0900
+++ b/samtools_v1_1.xml	Fri Nov 21 18:04:42 2014 +0900
@@ -3,8 +3,7 @@
     <requirement type="package" version="1.1">samtools</requirement>
   </requirements>
   <description>samtools version 1.1.</description>
-  <command interpreter="samtools index">$inputfile
-  2&gt;&amp;1 </command>
+  <command interpreter="samtools flagstat">$inputfile > $outfile</command>
   <inputs>
     <conditional name="command_type">
       <param name="command_type" type="select" label="Execute samtools command">
@@ -39,7 +38,7 @@
         <param format="bam" name="inputfile" type="data" label="index bam file"/>
       </when>
       <when value="flagstat">
-        <param format="bam" name="inputfile" type="data" label="Report bam stats"/>
+        <data format="txt" name="outfile" metadata_source="inputfile"/>
       </when>
     </conditional>
   </inputs>