Mercurial > repos > devteam > samtools_sort
comparison samtools_sort.xml @ 0:a430da4f04cd draft
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author | devteam |
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date | Tue, 21 Apr 2015 17:41:18 -0400 |
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children | cab3f8d35989 |
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-1:000000000000 | 0:a430da4f04cd |
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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> |