|
4
|
1 <tool id="samtools_sort" name="sort" version="1.0.3">
|
|
3
|
2 <requirements>
|
|
4
|
3 <requirement type="package" version="1.1">samtools</requirement>
|
|
3
|
4 </requirements>
|
|
|
5 <description>a BAM file</description>
|
|
|
6 <command>
|
|
|
7 samtools sort
|
|
|
8 $sort_mode
|
|
|
9 "${input1}" foo
|
|
|
10 2>&1 || echo "Error running samtools sort." >&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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
|
|
|
43
|
|
|
44 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
|
|
|
45
|
|
|
46 </help>
|
|
|
47 </tool>
|
