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comparison samtools_bedcov.xml @ 0:c04bee391baa draft

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author devteam
date Wed, 18 Mar 2015 16:43:50 -0400
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1 <tool id="samtools_bedcov" name="Calculate read depth" version="1.0.1">
2 <description>on BAM files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="version_command"></expand>
8 <expand macro="stdio"></expand>
9 <command><![CDATA[
10 for bamfile in
11 #for dataset in $input_bams:
12 "${dataset}"
13 #end for
14 ; do
15 if [ ! -f \$bamfile.bai ] ; then
16 ln -s \$bamfile && samtools index `basename \$bamfile` ;
17 else
18 ln -s \$bamfile && ln -s \$bamfile.bai ;
19 fi ;
20 done ;
21 samtools bedcov "${input_bed}"
22 #for dataset in $input_bams:
23 `basename "${dataset}"`
24 #end for
25 > "${output}"
26 ]]>
27 </command>
28 <inputs>
29 <param name="input_bed" type="data" format="bed" label="BED file" />
30 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
31 </inputs>
32 <outputs>
33 <data format="tabular" name="output" label="${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 </help>
55 <expand macro="citations"></expand>
56 </tool>
57