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comparison samtools_sort.xml @ 6:191cec7b989b draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:56:00 -0400
parents 346239545aa0
children 71d5c34fef4e
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5:346239545aa0 6:191cec7b989b
1 <tool id="samtools_sort" name="sort" version="1.0.3"> 1 <tool id="samtools_sort" name="Sort" version="2.0">
2 <requirements> 2 <description>BAM dataset</description>
3 <requirement type="package" version="1.1">samtools</requirement> 3 <macros>
4 </requirements> 4 <import>macros.xml</import>
5 <description>a BAM file</description> 5 </macros>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> 6 <expand macro="requirements"></expand>
7 <command>samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset</command> 7 <expand macro="stdio"></expand>
8 <stdio> 8 <expand macro="version_command"></expand>
9 <exit_code range="1:" level="fatal" description="Error" /> 9 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
10 </stdio>
11 <inputs> 10 <inputs>
12 <param name="input1" type="data" format="bam" label="BAM File" /> 11 <param name="input1" type="data" format="bam" label="BAM File" />
13 <param name="sort_mode" type="select" label="Sort by "> 12 <param name="sort_mode" type="select" label="Sort by ">
14 <option value="" selected="True">Chromosomal coordinates</option> 13 <option value="" selected="True">Chromosomal coordinates</option>
15 <option value="-n">Read names</option> 14 <option value="-n">Read names (-n)</option>
16 </param> 15 </param>
17 </inputs> 16 </inputs>
18 <outputs> 17 <outputs>
19 <data name="output1" format="bam" /> 18 <data name="output1" format="bam" />
20 </outputs> 19 </outputs>
21 <tests> 20 <tests>
22 <test> 21 <test>
23 <param name="input1" value="1.bam" ftype="bam" /> 22 <param name="input1" value="1.bam" ftype="bam" />
24 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> 23 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
25 </test> 24 </test>
25 <test>
26 <param name="input1" value="1.bam" ftype="bam" />
27 <param name="sort_mode" value="-n"/>
28 <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
29 </test>
26 </tests> 30 </tests>
27 <help> 31 <help>
28 32
29 **What it does** 33 **What it does**
30 34
31 This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names. 35 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
32 36
33 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
34
35 ------
36
37 **Citation**
38
39 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;`_
40
41 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
42 37
43 </help> 38 </help>
39 <expand macro="citations"></expand>
44 </tool> 40 </tool>