Mercurial > repos > bgruening > text_processing
comparison replace_text_in_column.xml @ 19:12615d397df7 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
author | bgruening |
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date | Thu, 29 Feb 2024 22:15:20 +0000 |
parents | a6f147a050a2 |
children |
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18:d698c222f354 | 19:12615d397df7 |
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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> |