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comparison replace_text_in_column.xml @ 26:f22a309187a3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
author bgruening
date Fri, 16 Aug 2024 10:41:17 +0000
parents bed2226b90f7
children 08cdbfffce67
comparison
equal deleted inserted replaced
25:cd83b5644eab 26:f22a309187a3
1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.3"> 1 <tool id="tp_replace_in_column" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>in a specific column</description> 2 <description>in a specific column</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="4.2.0">gawk</requirement> 8 <requirement type="package" version="5.3.0">gawk</requirement>
8 </requirements> 9 </requirements>
9 <version_command>awk --version | head -n 1</version_command> 10 <version_command>awk --version | head -n 1</version_command>
10 <command> 11 <command>
11 <![CDATA[ 12 <![CDATA[
12 awk 13 awk
17 '{ 18 '{
18 #for $replacement in $replacements: 19 #for $replacement in $replacements:
19 \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ; 20 \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ;
20 #end for 21 #end for
21 print \$0 ; }' 22 print \$0 ; }'
22 "$infile" 23 '$infile'
23 > "$outfile" 24 > '$outfile'
24 ]]> 25 ]]>
25 </command> 26 </command>
26 <inputs> 27 <inputs>
27 <param format="tabular" name="infile" type="data" label="File to process" /> 28 <param format="tabular" name="infile" type="data" label="File to process" />
28 <repeat name="replacements" title="Replacement" min="1"> 29 <repeat name="replacements" title="Replacement" min="1">
149 - **\|** Separates alternate possibilities. 150 - **\|** Separates alternate possibilities.
150 151
151 152
152 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. 153 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
153 154
154 @REFERENCES@
155 ]]> 155 ]]>
156 </help> 156 </help>
157 <expand macro="citations" /> 157 <expand macro="citations" />
158 </tool> 158 </tool>