|
8
|
1 <tool id="bigwig2_summary" name="bigWig2Summary">
|
|
|
2 <description> Extract summary information from a bigWig file across multiple genomic regions specified by the user. </description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.0">bigWigSummary</requirement>
|
|
|
5 <requirement type="package" version="1.0">fetchChromSizes</requirement>
|
|
|
6 <requirement type="package" version="1.0">bedClip</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command interpreter="bash">
|
|
|
9 bigwig2summary.sh -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output
|
|
|
10 </command>
|
|
|
11 <inputs>
|
|
|
12 <param name="input_bw" type="data" format="bigwig" label="Extract summary from" help="bigWig format."/>
|
|
|
13 <param name="input_bed" type="data" format="tabular" label="using genomic regions in" help="TAB delimited BED-like file."/>
|
|
|
14 <param name="bins" type="integer" value="1" label="Number of bins" help="Postitive integer"/>
|
|
|
15 <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" />
|
|
|
16 <param name="header" type="boolean" checked="False" truevalue="-e" falsevalue=" " label="Does the genomic region file contain a header?" />
|
|
|
17 <param name="type" type="select" label="Operation" help="">
|
|
|
18 <option value="mean">Average value in region (default)</option>
|
|
|
19 <option value="min">Minimum value in region</option>
|
|
|
20 <option value="max">Maximum value in region</option>
|
|
|
21 <option value="std">Standard deviation in region</option>
|
|
|
22 <option value="coverage">Percentage of region that is covered</option>
|
|
|
23 </param>
|
|
|
24 </inputs>
|
|
|
25
|
|
|
26 <outputs>
|
|
|
27 <data format="tabular" name="output"/>
|
|
|
28 </outputs>
|
|
|
29
|
|
|
30 <tests>
|
|
|
31 <test>
|
|
|
32 <param name="input_bw" value="1.bigwig" />
|
|
|
33 <param name="input_bed" value="1.bed" />
|
|
|
34 <param name="bins" value="3" />
|
|
|
35 <param name="assembly" value="hg19" />
|
|
11
|
36 <param name="header" value="true" />
|
|
8
|
37 <output name="output" file="1.tabular" />
|
|
|
38 </test>
|
|
|
39 <test>
|
|
|
40 <param name="input_bw" value="1.bigwig" />
|
|
|
41 <param name="input_bed" value="2.bed" />
|
|
|
42 <param name="bins" value="5" />
|
|
|
43 <param name="assembly" value="hg19" />
|
|
11
|
44 <param name="header" value="true" />
|
|
8
|
45 <output name="output" file="2.tabular" />
|
|
|
46 </test>
|
|
|
47 </tests>
|
|
|
48
|
|
|
49 <help>
|
|
|
50
|
|
|
51 This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file.
|
|
|
52
|
|
|
53 The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_, bedClip_ and fetchChromSizes_.
|
|
|
54
|
|
|
55 .. _bigWigSummary: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary
|
|
|
56
|
|
|
57 .. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip
|
|
|
58
|
|
|
59 -- _fetchChromSizes: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
|
|
|
60
|
|
|
61 -----
|
|
|
62
|
|
|
63 .. class:: infomark
|
|
|
64
|
|
|
65 The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed.
|
|
|
66
|
|
|
67 -----
|
|
|
68
|
|
|
69 **Example 1**
|
|
|
70
|
|
|
71 Input BED file::
|
|
|
72
|
|
|
73 chr19 50178708 50180708
|
|
|
74 chr6 90348174 90350174
|
|
|
75 chr16 58495848 58497848
|
|
|
76 chr5 180580242 180582242
|
|
|
77 chr9 120177017 120179017
|
|
|
78
|
|
|
79 Extract summary (*#* of bins = 3)::
|
|
|
80
|
|
|
81 0 0 0
|
|
|
82 0.144886 0 0
|
|
|
83 0.507327 1.14649 1.38456
|
|
|
84 0.221471 0.144886 0.309857
|
|
|
85 0.348944 0.426638 0.244495
|
|
|
86
|
|
|
87 **Example 2**
|
|
|
88
|
|
|
89 Input BED file (with strand information)::
|
|
|
90
|
|
|
91 chr19 50178708 50180708 NM_198318 0 + PRMT1
|
|
|
92 chr6 90348174 90350174 NM_020466 0 - LYRM2
|
|
|
93 chr16 58495848 58497848 NM_020465 0 + NDRG4
|
|
|
94 chr5 180580242 180582242 NM_206880 0 + OR2V2
|
|
|
95 chr9 120177017 120179017 NM_014010 0 - ASTN2
|
|
|
96
|
|
|
97 Extract summary (*#* of bins = 3)::
|
|
|
98
|
|
|
99 0 0 0
|
|
|
100 0 0 0.144886
|
|
|
101 0.507327 1.14649 1.38456
|
|
|
102 0.221471 0.144886 0.309857
|
|
|
103 0.244495 0.426638 0.348944
|
|
|
104
|
|
|
105 </help>
|
|
|
106 </tool>
|
