# HG changeset patch
# User devteam
# Date 1413477740 14400
# Node ID 346239545aa0f767e8d489c3c27fa14e7199753c
# Parent  1d317aeacef49f9ce65d2dd99ac9303d6794d914
Uploaded tool xml with improved command line.

diff -r 1d317aeacef4 -r 346239545aa0 samtools_sort.xml
--- a/samtools_sort.xml	Thu Oct 16 12:33:26 2014 -0400
+++ b/samtools_sort.xml	Thu Oct 16 12:42:20 2014 -0400
@@ -3,14 +3,11 @@
         <requirement type="package" version="1.1">samtools</requirement>
     </requirements>
     <description>a BAM file</description>
-    <command>
-        samtools sort
-            $sort_mode
-            "${input1}" foo
-            2&gt;&amp;1 || echo "Error running samtools sort." &gt;&amp;2
-            ;
-            mv foo.bam "${output1}"
-    </command>
+    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    <command>samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset</command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM File" />
         <param name="sort_mode" type="select" label="Sort by ">