# HG changeset patch # User martenson # Date 1410404775 14400 # Node ID 4cafbe1d2ea6533c73661ffb42e0be9e88ed8933 initial commit diff -r 000000000000 -r 4cafbe1d2ea6 samtools_sort.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_sort.xml Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,899 @@ + + + + + + + + + + + + + galaxytools/samtools_sort.xml at master · bgruening/galaxytools + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
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<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>
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+ + + + + + + + + + diff -r 000000000000 -r 4cafbe1d2ea6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,727 @@ + + + + + + + + + + + + + galaxytools/tool_dependencies.xml at master · bgruening/galaxytools + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Skip to content +
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<?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>
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