Mercurial > repos > iuc > bedtools
comparison genomeCoverageBed_histogram.xml @ 0:b8348686a0b9 draft
Imported from capsule None
author | iuc |
---|---|
date | Tue, 04 Nov 2014 01:45:04 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:b8348686a0b9 |
---|---|
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 $max | |
19 #end if | |
20 > '$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 <expand macro="citations" /> | |
68 </tool> |