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comparison bedtools-galaxy/genomeCoverageBed_histogram.xml @ 0:26c21c634c51

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author aaronquinlan
date Thu, 29 Dec 2011 10:20:07 -0500
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1 <tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.1.0">
2 <description>
3 </description>
4
5 <requirements>
6 <requirement type="binary">genomeCoverageBed</requirement>
7 </requirements>
8
9 <command>genomeCoverageBed
10 #if $input.ext == "bam"
11 -ibam '$input'
12 #else
13 -i '$input'
14 -g ${chromInfo}
15 #end if
16 #if str($max):
17 -max $max
18 #end if
19 &gt; '$output'
20 </command>
21
22 <inputs>
23 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
24 <param name="max" type="text" optional="true" label="Max depth" help="Combine all positions with a depth >= max into a single bin in the histogram."/>
25 </inputs>
26
27 <outputs>
28 <data format="tabular" name="output" metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
29 </outputs>
30
31 <help>
32 **What it does**
33
34 This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
35
36
37 ------
38
39 .. class:: warningmark
40
41 This tool requires that `bedtools`__ has been installed on your system.
42
43 .. class:: infomark
44
45 The output file will contain five columns:
46
47 * 1. Chromosome name (or 'genome' for whole-genome coverage)
48 * 2. Coverage depth
49 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
50 * 4. The size of chromosome (or entire genome) in base pairs
51 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
52
53 **Example Output**::
54
55 chr2L 0 1379895 23011544 0.0599653
56 chr2L 1 837250 23011544 0.0363839
57 chr2L 2 904442 23011544 0.0393038
58 chr2L 3 913723 23011544 0.0397072
59 chr2L 4 952166 23011544 0.0413778
60 chr2L 5 967763 23011544 0.0420555
61 chr2L 6 986331 23011544 0.0428624
62 chr2L 7 998244 23011544 0.0433801
63 chr2L 8 995791 23011544 0.0432735
64 chr2L 9 996398 23011544 0.0432999
65
66
67
68
69 ------
70
71 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
72
73 .. __: http://code.google.com/p/bedtools/
74 .. __: http://code.google.com/p/bedtools/
75 .. __: http://cphg.virginia.edu/quinlan/
76 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
77
78
79
80 </help>
81 </tool>