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comparison bedtools-galaxy/genomeCoverageBed_bedgraph.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_bedgraph" name="Create a BedGraph of genome coverage" version="0.1.0">
2
3 <description>
4 </description>
5
6 <requirements>
7 <requirement type="binary">genomeCoverageBed</requirement>
8 </requirements>
9
10 <command>genomeCoverageBed
11 #if $input.ext == "bam"
12 -ibam '$input'
13 #else
14 -i '$input'
15 -g ${chromInfo}
16 #end if
17
18 #if str($scale):
19 -scale $scale
20 #end if
21
22 -bg
23 $zero_regions
24 $split
25 $strand
26 &gt; '$output'
27 </command>
28
29 <inputs>
30 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
31 <validator type="unspecified_build" />
32 </param>
33
34 <param name="zero_regions" type="boolean" checked="true" truevalue="-bga" falsevalue="" label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported." />
35
36 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
37
38 <param name="strand" type="select" label="Calculate coverage based on">
39 <option value="">both strands combined</option>
40 <option value="-strand +">positive strand only</option>
41 <option value="-strand -">negative strand only</option>
42 </param>
43
44 <param name="scale" type="text" optional="true" label="Scale the coverage by a constant factor" help="Each BEDGRAPH coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)"/>
45 </inputs>
46
47 <outputs>
48 <data format="bedgraph" name="output" metadata_source="input" label="${input.name} (Genome Coverage BedGraph)" />
49 </outputs>
50 <help>
51
52
53 **What it does**
54
55 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
56
57 .. class:: warningmark
58
59 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).
60
61 .. class:: warningmark
62
63 This tool requires that `bedtools`__ has been installed on your system.
64
65 -----
66
67 **Example 1**
68
69 Input (BED format)-
70 Overlapping, un-sorted intervals::
71
72 chr1 140 176
73 chr1 100 130
74 chr1 120 147
75
76
77 Output (BedGraph format)-
78 Sorted, non-overlapping intervals, with coverage value on the 4th column::
79
80 chr1 100 120 1
81 chr1 120 130 2
82 chr1 130 140 1
83 chr1 140 147 2
84 chr1 147 176 1
85
86 -----
87
88 **Example 2 - with ZERO-Regions selected (assuming hg19)**
89
90 Input (BED format)-
91 Overlapping, un-sorted intervals::
92
93 chr1 140 176
94 chr1 100 130
95 chr1 120 147
96
97
98 Output (BedGraph format)-
99 Sorted, non-overlapping intervals, with coverage value on the 4th column::
100
101 chr1 0 100 0
102 chr1 100 120 1
103 chr1 120 130 2
104 chr1 130 140 1
105 chr1 140 147 2
106 chr1 147 176 1
107 chr1 176 249250621 0
108
109
110 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.`__
111
112 .. __: http://code.google.com/p/bedtools/
113 .. __: http://code.google.com/p/bedtools/
114 .. __: http://cphg.virginia.edu/quinlan/
115 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
116 </help>
117 </tool>