Mercurial > repos > jbrayet > samtools_1_2_docker

changeset 11:707978902d54 draft

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Uploaded
author jbrayet
date Wed, 25 Nov 2015 03:23:48 -0500
parents 9a4c773fb90d
children 25c5a69f5324
files samtools_sort.xml
diffstat 1 files changed, 40 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml	Wed Nov 25 03:23:48 2015 -0500
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+<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>