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comparison samtools_bedcov.xml @ 1:8c3472790020 draft

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author devteam
date Tue, 21 Apr 2015 15:05:45 -0400
parents c04bee391baa
children 12749212f61b
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0:c04bee391baa 1:8c3472790020
1 <tool id="samtools_bedcov" name="Calculate read depth" version="1.0.1"> 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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
7 <expand macro="version_command"></expand> 8 <expand macro="version_command"></expand>
8 <expand macro="stdio"></expand>
9 <command><![CDATA[ 9 <command><![CDATA[
10 for bamfile in 10 for bamfile in
11 #for dataset in $input_bams: 11 #for dataset in $input_bams:
12 "${dataset}" 12 "${dataset}"
13 #end for 13 #end for
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 </help> 54 </help>
55 <expand macro="citations"></expand> 55 <expand macro="citations"></expand>
56 </tool> 56 </tool>
57 57