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comparison replace_text_in_column.xml @ 6:60edf2f8c28f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:09:05 -0400
parents 20344ce0c811
children 74a8bef53a00
comparison
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5:20344ce0c811 6:60edf2f8c28f
1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.0"> 1 <tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.1">
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 <requirements> 6 <requirements>
8 </requirements> 8 </requirements>
9 <version_command>awk --version | head -n 1</version_command> 9 <version_command>awk --version | head -n 1</version_command>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 awk 12 awk
13 -v OFS=" " 13 -v OFS="\t"
14 -v FS="\t"
14 --re-interval 15 --re-interval
15 --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }' 16 --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }'
16 "$infile" 17 "$infile"
17 > "$outfile" 18 > "$outfile"
18 ]]> 19 ]]>
130 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. 131 **Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
131 132
132 @REFERENCES@ 133 @REFERENCES@
133 ]]> 134 ]]>
134 </help> 135 </help>
136 <expand macro="citations" />
135 </tool> 137 </tool>