# HG changeset patch
# User jbrayet
# Date 1448439828 18000
# Node ID 707978902d54858ca81513541266d8b3580b6961
# Parent  9a4c773fb90dcee5dd3fffde93a1b47160bcd4e8
Uploaded

diff -r 9a4c773fb90d -r 707978902d54 samtools_sort.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml	Wed Nov 25 03:23:48 2015 -0500
@@ -0,0 +1,40 @@
+<tool id="samtools_sort" name="Sort" version="2.0">
+    <description>BAM dataset</description>
+    <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM File" />
+        <param name="sort_mode" type="select" label="Sort by ">
+            <option value="" selected="True">Chromosomal coordinates</option>
+            <option value="-n">Read names (-n)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="bam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bam" ftype="bam" />
+            <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
+        </test>
+        <test>
+            <param name="input1" value="1.bam" ftype="bam" />
+            <param name="sort_mode" value="-n"/>
+            <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
+
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>