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comparison genomeCoverageBed_histogram.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="@WRAPPER_VERSION@.0">
2 <description>
3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <command>
10 genomeCoverageBed
11 #if $input.ext == "bam"
12 -ibam '$input'
13 #else
14 -i '$input'
15 -g ${chromInfo}
16 #end if
17 #if str($max):
18 -max $max
19 #end if
20 &gt; '$output'
21 </command>
22
23 <inputs>
24 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
25 <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."/>
26 </inputs>
27
28 <outputs>
29 <data format="tabular" name="output" metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
30 </outputs>
31
32 <help>
33 **What it does**
34
35 This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
36
37
38 ------
39
40
41 .. class:: infomark
42
43 The output file will contain five columns:
44
45 * 1. Chromosome name (or 'genome' for whole-genome coverage)
46 * 2. Coverage depth
47 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
48 * 4. The size of chromosome (or entire genome) in base pairs
49 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
50
51 **Example Output**::
52
53 chr2L 0 1379895 23011544 0.0599653
54 chr2L 1 837250 23011544 0.0363839
55 chr2L 2 904442 23011544 0.0393038
56 chr2L 3 913723 23011544 0.0397072
57 chr2L 4 952166 23011544 0.0413778
58 chr2L 5 967763 23011544 0.0420555
59 chr2L 6 986331 23011544 0.0428624
60 chr2L 7 998244 23011544 0.0433801
61 chr2L 8 995791 23011544 0.0432735
62 chr2L 9 996398 23011544 0.0432999
63
64
65 @REFERENCES@
66 </help>
67 </tool>