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comparison samtools_bedcov.xml @ 1:4f7acd7af617 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:54:07 -0400
parents 6ffa7e68dc1f
children e371922c38e8
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0:6ffa7e68dc1f 1:4f7acd7af617
1 <tool id="samtools_bedcov" name="Calculate read depth" version="1.0.0"> 1 <tool id="samtools_bedcov" name="BedCov" version="2.0">
2 <description>on BAM files</description> 2 <description>calculate read depth for a set of genomic intervals</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.1">samtools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> 6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
7 <command><![CDATA[ 9 <command><![CDATA[
8 for bamfile in 10 for bamfile in
9 #for dataset in $input_bams: 11 #for dataset in $input_bams:
10 "${dataset}" 12 "${dataset}"
11 #end for 13 #end for
19 samtools bedcov "${input_bed}" 21 samtools bedcov "${input_bed}"
20 #for dataset in $input_bams: 22 #for dataset in $input_bams:
21 `basename "${dataset}"` 23 `basename "${dataset}"`
22 #end for 24 #end for
23 > "${output}" 25 > "${output}"
24 ]]></command> 26 ]]>
25 <stdio> 27 </command>
26 <exit_code range="1:" level="fatal" description="Error" />
27 </stdio>
28 <inputs> 28 <inputs>
29 <param name="input_bed" type="data" format="bed" label="BED file" /> 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" /> 30 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" />
31 </inputs> 31 </inputs>
32 <outputs> 32 <outputs>
45 </test> 45 </test>
46 </tests> 46 </tests>
47 <help> 47 <help>
48 **What it does** 48 **What it does**
49 49
50 This tool runs the ``samtools bedcov`` command in the SAMtools toolkit. 50 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
51 51
52 Show read depth per BED region. 52 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
53 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> 54 </help>
55 <expand macro="citations"></expand>
61 </tool> 56 </tool>
62 57