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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
author blankenberg
date Fri, 07 Sep 2018 10:29:30 -0400
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1 <tool id="column_regex_substitution" name="Column substitution" version="0.0.1">
2 <description>by regular expressions</description>
3 <requirements>
4 <requirement type="package" version="2.7">python</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 <exit_code range=":-1" />
9 </stdio>
10 <version_command>python column_regex_substitution.py --version</version_command>
11 <command><![CDATA[
12 #import pipes
13 python '$__tool_directory__/column_regex_substitution.py'
14 --input '${input_tabular}'
15 --pattern ${pipes.quote( str( $pattern ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""'}
16 --replacement ${ pipes.quote( str( $replacement ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""' }
17 --columns '${ $columns or "" }'
18 --output '${outfile}'
19 #if $input_tabular.metadata.delimiter:
20 --delimiter ${ pipes.quote( str( $input_tabular.unsanitized.metadata.delimiter ) ) }
21 #end if
22 --column_offset '-1'
23 ]]>
24 </command>
25 <inputs>
26 <param name="input_tabular" type="data" format="txt" label="File to perform substitution on" />
27 <param name="pattern" type="text" label="Pattern to Match">
28 <sanitizer sanitize="False" />
29 </param>
30 <param name="replacement" type="text" label="Replacement">
31 <sanitizer sanitize="False" />
32 </param>
33 <param name="columns" label="Columns for substitution" type="data_column" data_ref="input_tabular" optional="True" multiple="True" help="Selecting no columns will target all columns"/>
34 </inputs>
35 <outputs>
36 <data name="outfile" format_source="input_tabular" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="input_tabular" ftype="tabular" value="column_regex_substitution_in.tabular"/>
41 <param name="pattern" value="^$"/>
42 <param name="replacement" value="."/>
43 <param name="columns" value="1"/>
44 <output name="outfile" ftype="tabular" file="column_regex_substitution_out.tabular" />
45 </test>
46 </tests>
47 <help><![CDATA[
48 **What it does**
49
50 Use regular expressions (regex) to substitute field values. Datasets that do not have a metadata delimiter value will be treated as a single column per row.
51
52 This tool makes use of Python's `re.sub functionality <https://docs.python.org/2/library/re.html#re.sub>`_.
53
54 ]]>
55 </help>
56 <citations></citations>
57 </tool>