Mercurial > repos > xuebing > sharplabtool
comparison tools/regVariation/maf_cpg_filter.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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 <command interpreter="python"> | |
4 maf_cpg_filter.py | |
5 $input | |
6 $out_file1 | |
7 $masksite.type | |
8 #if $masksite.type == "CpG": | |
9 $masksite.definition | |
10 #else: | |
11 "NA" | |
12 #end if | |
13 -m $mask_char | |
14 </command> | |
15 <inputs> | |
16 <page> | |
17 <param format="maf" name="input" type="data" label="Select data"/> | |
18 <param name="mask_char" size="5" type="select" label="Mask character"> | |
19 <option value="0" selected="true">#</option> | |
20 <option value="1">$</option> | |
21 <option value="2">^</option> | |
22 <option value="3">*</option> | |
23 <option value="4">?</option> | |
24 <option value="5">N</option> | |
25 </param> | |
26 <conditional name="masksite"> | |
27 <param name="type" size="5" type="select" label="Sites to be masked"> | |
28 <option value="CpG" selected="true">CpG sites</option> | |
29 <option value="nonCpG">non-CpG sites</option> | |
30 </param> | |
31 <when value="CpG"> | |
32 <param name="definition" size="5" type="select" label="Definition"> | |
33 <option value="0" selected="true">Inclusive</option> | |
34 <option value="1">Restricted</option> | |
35 </param> | |
36 </when> | |
37 <when value="nonCpG" /> | |
38 </conditional> | |
39 </page> | |
40 </inputs> | |
41 <outputs> | |
42 <data format="maf" name="out_file1" metadata_source="input"/> | |
43 </outputs> | |
44 <requirements> | |
45 <requirement type="python-module">numpy</requirement> | |
46 </requirements> | |
47 <tests> | |
48 <test> | |
49 <param name="input" value="6.maf"/> | |
50 <param name="mask_char" value="0"/> | |
51 <param name="type" value="CpG" /> | |
52 <param name="definition" value="0" /> | |
53 <output name="out_file1" file="6_mask_cpg.maf"/> | |
54 </test> | |
55 <test> | |
56 <param name="input" value="6.maf"/> | |
57 <param name="mask_char" value="0"/> | |
58 <param name="type" value="nonCpG" /> | |
59 <output name="out_file1" file="6_mask_noncpg.maf"/> | |
60 </test> | |
61 </tests> | |
62 <help> | |
63 | |
64 .. class:: infomark | |
65 | |
66 **What it does** | |
67 | |
68 This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. | |
69 | |
70 ----- | |
71 | |
72 .. class:: warningmark | |
73 | |
74 **Note** | |
75 | |
76 *Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species. | |
77 | |
78 *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. | |
79 | |
80 For more information on CpG site definitions, please refer this article_. | |
81 | |
82 .. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565 | |
83 | |
84 </help> | |
85 | |
86 | |
87 </tool> |