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comparison samtools_bedcov.xml @ 0:6ffa7e68dc1f draft

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Uploaded initial tool definition.
author devteam
date Mon, 27 Oct 2014 12:42:42 -0400
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1 <tool id="samtools_bedcov" name="Calculate read depth" version="1.0.0">
2 <description>on BAM files</description>
3 <requirements>
4 <requirement type="package" version="1.1">samtools</requirement>
5 </requirements>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
7 <command><![CDATA[
8 for bamfile in
9 #for dataset in $input_bams:
10 "${dataset}"
11 #end for
12 ; do
13 if [ ! -f \$bamfile.bai ] ; then
14 ln -s \$bamfile && samtools index `basename \$bamfile` ;
15 else
16 ln -s \$bamfile && ln -s \$bamfile.bai ;
17 fi ;
18 done ;
19 samtools bedcov "${input_bed}"
20 #for dataset in $input_bams:
21 `basename "${dataset}"`
22 #end for
23 > "${output}"
24 ]]></command>
25 <stdio>
26 <exit_code range="1:" level="fatal" description="Error" />
27 </stdio>
28 <inputs>
29 <param name="input_bed" type="data" format="bed" label="BED file" />
30 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
31 </inputs>
32 <outputs>
33 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
34 </outputs>
35 <tests>
36 <test>
37 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
38 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
39 <output name="output" file="samtools_bedcov_out1.tab" />
40 </test>
41 <test>
42 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
43 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
44 <output name="output" file="samtools_bedcov_out2.tab" />
45 </test>
46 </tests>
47 <help>
48 **What it does**
49
50 This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
51
52 Show read depth per BED region.
53
54 **Citation**
55
56 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;`_
57
58
59 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
60 </help>
61 </tool>
62