# HG changeset patch
# User soh.ishiguro3914@gmail.com
# Date 1416554717 -32400
# Node ID 9390fca875f941d040dc770f4e577b1d5c7731fc

Initial commit

diff -r 000000000000 -r 9390fca875f9 samtools_v1_1.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_v1_1.xml	Fri Nov 21 16:25:17 2014 +0900
@@ -0,0 +1,36 @@
+<tool id="samtools_v1_1" name="samtools_v1_1" version="1.1">
+  <requirements>
+    <requirement type="package" version="1.1">samtools</requirement>
+  </requirements>
+  <description>samtools version 1.1.</description>
+  <inputs>
+    <conditional name="command_type">
+      <param name="command_type" type="select" label="Execute samtools command">
+        <option value="view">view</option>
+        <option value="sort">sort</option>
+    	<option value="mpileup">mpileup</option>
+	    <option value="depth">depth</option>
+    	<option value="faidx">faidx</option>
+        <option value="tview">tview</option>
+	    <option value="index">index</option>
+        <option value="idxstats">idxstats</option>
+        <option value="fixmate">fixmate</option>
+        <option value="flagstat">flagstat</option>
+        <option value="calmd">calmd</option>
+        <option value="merge">merge</option>
+        <option value="rmdup">rmdup</option>
+        <option value="reheader">reheader</option>
+        <option value="cat">cat</option>
+        <option value="bedcov">bedcov</option>
+        <option value="targetcut">targetcut</option>
+        <option value="phase">phase</option>
+        <option value="bamshuf">bamshuf</option>
+      </param>
+      <when value="sort">
+        <param format="sam" name="inputfile" type="data" label="sort alignment file">
+          <option value="hg19">hg19</option>
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+</tool>