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comparison samtools_sort.xml @ 3:5e12c7427fa3

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author martenson <cech.marten@gmail.com>
date Wed, 10 Sep 2014 23:12:14 -0400
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2:5c01430e6e76 3:5e12c7427fa3
1 <tool id="samtools_sort" name="sort" version="1.0.2">
2 <requirements>
3 <requirement type="package" version="0.1.19">samtools</requirement>
4 </requirements>
5 <description>a BAM file</description>
6 <command>
7 samtools sort
8 $sort_mode
9 "${input1}" foo
10 2&gt;&amp;1 || echo "Error running samtools sort." &gt;&amp;2
11 ;
12 mv foo.bam "${output1}"
13 </command>
14 <inputs>
15 <param name="input1" type="data" format="bam" label="BAM File" />
16 <param name="sort_mode" type="select" label="Sort by ">
17 <option value="" selected="True">Chromosomal coordinates</option>
18 <option value="-n">Read names</option>
19 </param>
20 </inputs>
21 <outputs>
22 <data name="output1" format="bam" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="input1" value="1.bam" ftype="bam" />
27 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
28 </test>
29 </tests>
30 <help>
31
32 **What it does**
33
34 This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.
35
36 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
37
38 ------
39
40 **Citation**
41
42 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;`_
43
44 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
45
46 </help>
47 </tool>