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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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12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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1 <tool id="column_regex_substitution" name="Column substitution" version="0.0.1">
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2 <description>by regular expressions</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 <exit_code range=":-1" />
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9 </stdio>
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10 <version_command>python column_regex_substitution.py --version</version_command>
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11 <command><![CDATA[
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12 #import pipes
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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13 python '$__tool_directory__/column_regex_substitution.py'
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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14 --input '${input_tabular}'
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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15 --pattern ${pipes.quote( str( $pattern ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""'}
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16 --replacement ${ pipes.quote( str( $replacement ).replace('\\','\\\\').decode( 'string_escape' ) ) or '""' }
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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17 --columns '${ $columns or "" }'
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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18 --output '${outfile}'
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19 #if $input_tabular.metadata.delimiter:
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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20 --delimiter ${ pipes.quote( str( $input_tabular.unsanitized.metadata.delimiter ) ) }
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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21 #end if
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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22 --column_offset '-1'
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="input_tabular" type="data" format="txt" label="File to perform substitution on" />
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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27 <param name="pattern" type="text" label="Pattern to Match">
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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28 <sanitizer sanitize="False" />
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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29 </param>
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30 <param name="replacement" type="text" label="Replacement">
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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31 <sanitizer sanitize="False" />
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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32 </param>
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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"/>
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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34 </inputs>
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35 <outputs>
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36 <data name="outfile" format_source="input_tabular" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input_tabular" ftype="tabular" value="column_regex_substitution_in.tabular"/>
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41 <param name="pattern" value="^$"/>
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42 <param name="replacement" value="."/>
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43 <param name="columns" value="1"/>
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44 <output name="outfile" ftype="tabular" file="column_regex_substitution_out.tabular" />
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 **What it does**
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49
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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.
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51
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52 This tool makes use of Python's `re.sub functionality <https://docs.python.org/2/library/re.html#re.sub>`_.
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53
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54 ]]>
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55 </help>
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56 <citations></citations>
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57 </tool>