# HG changeset patch
# User soh.ishiguro3914@gmail.com
# Date 1416557200 -32400
# Node ID ff0439a80cdd1c3eb438fd13076c046cdadaf6ef
# Parent  7019465fef450798a0f63a5e4bdbdfacdf53839a
samtools_v1_1.xml

diff -r 7019465fef45 -r ff0439a80cdd samtools_v1_1.xml
--- a/samtools_v1_1.xml	Fri Nov 21 16:38:38 2014 +0900
+++ b/samtools_v1_1.xml	Fri Nov 21 17:06:40 2014 +0900
@@ -3,6 +3,7 @@
     <requirement type="package" version="1.1">samtools</requirement>
   </requirements>
   <description>samtools version 1.1.</description>
+  <command interpreter="samtools index">$inputfile</command>
   <inputs>
     <conditional name="command_type">
       <param name="command_type" type="select" label="Execute samtools command">
@@ -34,13 +35,7 @@
         </param>
       </when>
       <when value="index">
-        <param format="bam" name="inputfile" type="data" label="index file"/>
-      </when>
-      <when value="view">
-        <param format="bam" name="inputfile" type="data" label="view file"/>
-      </when>
-      <when value="mpileup">
-        <param format="bam" name="inputfile" type="data" label="mpileup file"/>
+        <param format="bam" name="inputfile" type="data" label="index bam file"/>
       </when>
     </conditional>
   </inputs>