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comparison column_extract.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="column_select" name="Column Select" version="1">
2
3 <description> extract/rearrange columns from a tab-delimited file </description>
4 <code file="getcolumnnames.py"/>
5
6 <command interpreter="bash">
7 column_extract.sh
8 $infile
9 $outputfile
10 $removeheader
11 #for $c in $go.columns
12 ${c.column}
13 #end for
14 </command>
15
16 <outputs>
17 <data format="tabular" name="outputfile" label="${sample} Column extract on ${on_string}"/>
18 </outputs>
19
20 <inputs>
21
22 <param name="infile" type="data" label="Select file to extract columns from" help="Must be a tab-separated file with a 1-line header"/>
23 <param name="removeheader" type="boolean" truevalue="Y" falsevalue="N" selected="false" label="Remove header?" help="If selected, any lines starting with # and any empty lines will not be output."/>
24
25 <conditional name="go">
26 <param name="ready" type="select" label="Ready to select columns?" help="Set to NO and back to YES after changing input file">
27 <option value="no" selected="True">no</option>
28 <option value="yes">yes</option>
29 </param>
30
31 <when value="yes">
32 <repeat name="columns" title="Column" min="1">
33 <!-- <param name="col" type="data_column" data_ref="infile" multiple="False" label="Column from file to output" /> -->
34 <param name="column" type="select" dynamic_options="get_headers(infile)" multiple="False" label="Select Column" />
35 </repeat>
36 </when>
37 </conditional>
38
39 <param name="sample" type="text" value="" label="Sample Name" help="Optional. For file naming purposes only"/>
40
41 </inputs>
42
43 <help>
44
45
46 **What it does**
47 Outputs columns of input file in order specified by user. Columns not selected will not be output.
48
49 </help>
50 </tool>