Mercurial > repos > devteam > samtools_sort

changeset 5:346239545aa0 draft

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Uploaded tool xml with improved command line.
author devteam
date Thu, 16 Oct 2014 12:42:20 -0400
parents 1d317aeacef4
children 191cec7b989b
files samtools_sort.xml
diffstat 1 files changed, 5 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- 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 ">