Mercurial > repos > devteam > maf_cpg_filter
comparison maf_cpg_filter.xml @ 0:7f2a12cb047d draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 10:51:18 -0400 |
parents | |
children | e5b0c8ca1399 |
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-1:000000000000 | 0:7f2a12cb047d |
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1 <tool id="cpgFilter" name="Mask CpG/non-CpG sites" version="1.0.0"> | |
2 <description> from MAF file</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 maf_cpg_filter.py | |
8 $input | |
9 $out_file1 | |
10 $masksite.type | |
11 #if $masksite.type == "CpG": | |
12 $masksite.definition | |
13 #else: | |
14 "NA" | |
15 #end if | |
16 -m $mask_char | |
17 </command> | |
18 <inputs> | |
19 <page> | |
20 <param format="maf" name="input" type="data" label="Select data"/> | |
21 <param name="mask_char" size="5" type="select" label="Mask character"> | |
22 <option value="0" selected="true">#</option> | |
23 <option value="1">$</option> | |
24 <option value="2">^</option> | |
25 <option value="3">*</option> | |
26 <option value="4">?</option> | |
27 <option value="5">N</option> | |
28 </param> | |
29 <conditional name="masksite"> | |
30 <param name="type" size="5" type="select" label="Sites to be masked"> | |
31 <option value="CpG" selected="true">CpG sites</option> | |
32 <option value="nonCpG">non-CpG sites</option> | |
33 </param> | |
34 <when value="CpG"> | |
35 <param name="definition" size="5" type="select" label="Definition"> | |
36 <option value="0" selected="true">Inclusive</option> | |
37 <option value="1">Restricted</option> | |
38 </param> | |
39 </when> | |
40 <when value="nonCpG" /> | |
41 </conditional> | |
42 </page> | |
43 </inputs> | |
44 <outputs> | |
45 <data format="maf" name="out_file1" metadata_source="input"/> | |
46 </outputs> | |
47 <requirements> | |
48 <requirement type="python-module">numpy</requirement> | |
49 </requirements> | |
50 <tests> | |
51 <test> | |
52 <param name="input" value="6.maf"/> | |
53 <param name="mask_char" value="0"/> | |
54 <param name="type" value="CpG" /> | |
55 <param name="definition" value="0" /> | |
56 <output name="out_file1" file="6_mask_cpg.maf"/> | |
57 </test> | |
58 <test> | |
59 <param name="input" value="6.maf"/> | |
60 <param name="mask_char" value="0"/> | |
61 <param name="type" value="nonCpG" /> | |
62 <output name="out_file1" file="6_mask_noncpg.maf"/> | |
63 </test> | |
64 </tests> | |
65 <help> | |
66 | |
67 .. class:: infomark | |
68 | |
69 **What it does** | |
70 | |
71 This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. | |
72 | |
73 ----- | |
74 | |
75 .. class:: warningmark | |
76 | |
77 **Note** | |
78 | |
79 *Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species. | |
80 | |
81 *Restricted definition* considers sites to be CpG if they are CG in at least one of the species, however, sites that are part of overlapping CpGs are excluded. | |
82 | |
83 For more information on CpG site definitions, please refer this article_. | |
84 | |
85 .. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565 | |
86 | |
87 </help> | |
88 | |
89 | |
90 </tool> |