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changeset 3:5e12c7427fa3

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new initial commit
author martenson <cech.marten@gmail.com>
date Wed, 10 Sep 2014 23:12:14 -0400
parents 5c01430e6e76
children 1d317aeacef4
files samtools_sort.xml test-data/1.bam test-data/1_sort.bam tool_dependencies.xml
diffstat 4 files changed, 53 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_sort.xml	Wed Sep 10 23:12:14 2014 -0400
@@ -0,0 +1,47 @@
+<tool id="samtools_sort" name="sort" version="1.0.2">
+    <requirements>
+        <requirement type="package" version="0.1.19">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>
+    <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</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>
+    </tests>
+    <help>
+
+**What it does**
+
+This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.
+
+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+    </help>
+</tool>
Binary file test-data/1.bam has changed
Binary file test-data/1_sort.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 10 23:12:14 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository name="package_samtools_0_1_19" owner="devteam" />
+    </package>
+</tool_dependency>