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comparison chrprefix.xml @ 0:e77c9484b2d0 draft default tip

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author saskia-hiltemann
date Thu, 22 Oct 2015 09:18:30 -0400
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1 <tool id="chr_prefix" name="Add/Remove chr prefix" version="1">
2
3 <description> add or remove chr prefix from a column </description>
4
5 <code file="getcolumnnames.py"/>
6
7 <command interpreter="bash">
8 chrprefix.sh
9 $infile
10 "${go.column}"
11 $addremove
12 $outputfile
13 </command>
14
15 <outputs>
16 <data format="tabular" name="outputfile" label="${sample} - chr-prefix on ${on_string}"/>
17 </outputs>
18
19 <inputs>
20
21 <param name="infile" type="data" label="Select inputfile" help="must be a tab-delimited file with a 1-line header" />
22 <conditional name="go">
23 <param name="ready" type="select" label="Ready to select column?" help="Set to NO and back to YES after changing input file">
24 <option value="no" selected="True">no</option>
25 <option value="yes">yes</option>
26 </param>
27
28 <when value="yes">
29 <param name="column" type="select" dynamic_options="get_headers(infile)" multiple="False" label="Select Column" />
30 </when>
31 </conditional>
32
33 <param name="addremove" type="select" label="Add or remove the chr prefix?">
34 <option value="add">Add</option>
35 <option value="remove">Remove</option>
36 </param>
37 <param name="sample" type="text" value="" label="Output File Name" help="Optional."/>
38
39 </inputs>
40
41 <help>
42
43 **What it does**
44 removes or adds the "chr" prefix in a column of a file. Some tools expect you to indicate chromosomes as "chr1,chr2,chrX", while others expect only 1,2,X as input. This tool allows you to easily switch notations
45
46 </help>
47 </tool>