root/galaxy-central/tools/regVariation/maf_cpg_filter.xml

リビジョン 2, 2.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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      <param name="definition" value="NA" />
60      <output name="out_file1" file="6_mask_noncpg.maf"/>
61    </test>
62  </tests>
63 <help>
64
65.. class:: infomark
66
67**What it does**
68
69This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file.
70
71-----
72
73.. class:: warningmark
74
75**Note**
76
77*Inclusive definition* defines CpG sites as those sites that are CG in at least one of the species.
78
79*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.
80
81For more information on CpG site definitions, please refer this article_.
82
83.. _article: http://mbe.oxfordjournals.org/cgi/content/full/23/3/565
84
85  </help> 
86
87
88</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。