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author pmac
date Wed, 01 Jun 2016 03:48:29 -0400
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1 <tool id="map_chromosomes" name="Convert between UCSC and ensembl chromosome names" version="0.0.1">
2 <description>chromosome representation</description>
3 <command interpreter="perl">map_chromosomes.pl $input1 $col $delimiter ${map.fields.path} $out_file1</command>
4 <inputs>
5 <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
6 <param name="col" type="integer" value="1" label="Column containing chromosome ids"/>
7 <param name="delimiter" type="select" label="Delimited by">
8 <option value="TAB">Tab</option>
9 <option value="SPACE">Whitespace</option>
10 <option value="DOT">Dot</option>
11 <option value="COMMA">Comma</option>
12 <option value="DASH">Dash</option>
13 <option value="UNDERSCORE">Underscore</option>
14 <option value="PIPE">Pipe</option>
15 </param>
16 <param name="map" type="select" label="Select a mapping file" help="Ensure you select the correct mapping file">
17 <options from_data_table="map_chromosomes">
18 <filter type="sort_by" column="2"/>
19 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
20 </options>
21 </param>
22 </inputs>
23 <outputs>
24 <data name="out_file1" format="input" metadata_source="input1"/>
25 </outputs>
26
27 <tests>
28 <test>
29 <param name="col" value="1"/>
30 <param name="delimiter" value="TAB"/>
31 <param name="map" value="hg19 UCSC to ensembl"/>
32 <param name="input1" value="map_chrom_ucsc.txt" dbkey="hg19" />
33 <output name="out_file1" file="map_chrom_ensembl.txt"/>
34 </test>
35 <test>
36 <param name="col" value="1"/>
37 <param name="delimiter" value="TAB"/>
38 <param name="map" value="hg19 ensembl to UCSC"/>
39 <param name="input1" value="map_chrom_ensembl.txt" dbkey="hg19" />
40 <output name="out_file1" file="map_chrom_ucsc.txt"/>
41 </test>
42 </tests>
43 <help>
44
45
46 **What it does**
47
48 Converts a column between the UCSC and ensembl representation of chromosomes.
49
50 .. class:: warningmark
51
52 **Warning any lines containing chromosomes that don't map or are invalid will be removed**
53
54 -----
55
56 **Example 1**
57
58 Converting this dataset::
59
60 chr21 12 123
61 chrM 45 345
62
63 by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 UCSC to ensembl** will produce::
64
65 21 12 123
66 MT 45 345
67
68 -----
69
70 **Example 2**
71
72 Converting this dataset::
73
74 21 12 123
75 MT 45 345
76
77 by setting **Column** to *1*, **Delimiter** to *Tab* and **Mapping** file to *hg19 ensembl to UCSC** will produce::
78
79 chr21 12 123
80 chrM 45 345
81
82
83 </help>
84 </tool>