28
|
1 <tool id="parsewig" name="WIG parser">
|
|
2 <command interpreter="bash">
|
|
3 parsewig.sh
|
|
4 input=$input
|
|
5 extract=$extract
|
|
6 #if str($selectContext.context) == "yes":
|
|
7 context="$selectContext.cpg,$selectContext.chg,$selectContext.chh"
|
|
8 #end if
|
|
9 depth=$depth
|
|
10 cov_out=$coverage
|
|
11 meth_out=$methylation
|
|
12 </command>
|
|
13 <inputs>
|
|
14 <param name="input" format="text" type="data" label="Methylation calling output file" />
|
|
15 <param name="extract" type="select" label="Which files should be extracted?">
|
|
16 <option value="m">Methylation</option>
|
|
17 <option value="c">Coverage</option>
|
|
18 <option value="b">Methylation and Coverage</option>
|
|
19 </param>
|
|
20
|
|
21 <conditional name="selectContext">
|
|
22 <param name="context" type="select" label="Limit the output to a specific context?">
|
|
23 <option value="no">No, report all</option>
|
|
24 <option value="yes">Yes</option>
|
|
25 </param>
|
|
26 <when value="no" />
|
|
27 <when value="yes">
|
|
28 <param name="cpg" type="boolean" truevalue="cpg" falsevalue="" checked="False" label="report loci in CpG context" />
|
|
29 <param name="chg" type="boolean" truevalue="chg" falsevalue="" checked="False" label="report loci in CHG context" />
|
|
30 <param name="chh" type="boolean" truevalue="chh" falsevalue="" checked="False" label="report loci in CHH context" />
|
|
31 </when>
|
|
32 </conditional>
|
|
33 <param name="depth" type="integer" value="1" label="Minimum sequencing depth to report loci" />
|
|
34 </inputs>
|
|
35 <outputs>
|
|
36 <data name="methylation" format ="wig" label="WIG parser: Methylation">
|
|
37 <filter>(extract == 'm' or extract == 'b' )</filter>
|
|
38 </data>
|
|
39 <data name="coverage" format ="wig" label="WIG parser: Coverage">
|
|
40 <filter>(extract == 'c' or extract == 'b' )</filter>
|
|
41 </data>
|
|
42
|
|
43 </outputs>
|
|
44 <help>
|
|
45 **What it does**
|
|
46
|
|
47 This is a parser for the output files coming from "Bismark Methylation Caller" or "BSMAP Methylation Caller". The data is parsed into WIGGLE format.
|
|
48
|
|
49 Other options:
|
|
50 - define context of cytosines should be reported (CpG, CHG, CHH)
|
|
51 - define the minimum sequencing depth (coverage) of cytosines should be reported
|
|
52
|
|
53 **Output format**
|
|
54
|
|
55 You get one file for methylation and/or coverage (depending on what you choose under "Which files should be etracted?").
|
|
56
|
|
57 The output has the following columns::
|
|
58
|
|
59 Column Description
|
|
60 ------ --------------------------------------------------------
|
|
61 1 cytosine position
|
|
62 2 methylation state (in %) / coverage
|
|
63 (positive value for plus strand / negative value for minus strand)
|
|
64
|
|
65 </help>
|
|
66 </tool>
|
|
67
|