|
0
|
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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
|
|
|
57
|
|
|
58
|
|
|
59 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
|
|
|
60 </help>
|
|
|
61 </tool>
|
|
|
62
|
