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comparison samtools_sort.xml @ 0:a430da4f04cd draft

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author devteam
date Tue, 21 Apr 2015 17:41:18 -0400
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1 <tool id="samtools_sort" name="Sort" version="2.0">
2 <description>BAM dataset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
9 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
10 <inputs>
11 <param name="input1" type="data" format="bam" label="BAM File" />
12 <param name="sort_mode" type="select" label="Sort by ">
13 <option value="" selected="True">Chromosomal coordinates</option>
14 <option value="-n">Read names (-n)</option>
15 </param>
16 </inputs>
17 <outputs>
18 <data name="output1" format="bam" />
19 </outputs>
20 <tests>
21 <test>
22 <param name="input1" value="1.bam" ftype="bam" />
23 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
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>
30 </tests>
31 <help>
32
33 **What it does**
34
35 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
36
37
38 </help>
39 <expand macro="citations"></expand>
40 </tool>