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comparison replace_text_in_line.xml @ 27:08cdbfffce67 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
author bgruening
date Fri, 07 Mar 2025 20:43:41 +0000
parents f22a309187a3
children 5907d248dee3
comparison
equal deleted inserted replaced
26:f22a309187a3 27:08cdbfffce67
12 <![CDATA[ 12 <![CDATA[
13 sed 13 sed
14 -r 14 -r
15 --sandbox 15 --sandbox
16 #for $replacement in $replacements: 16 #for $replacement in $replacements:
17 -e '$replacement.sed_options'
17 -e 18 -e
18 's/$replacement.find_pattern/$replacement.replace_pattern/g' 19 's/$replacement.find_pattern/$replacement.replace_pattern/g'
19 #end for 20 #end for
20 '$infile' 21 '$infile'
21 > '$outfile' 22 > '$outfile'
45 </valid> 46 </valid>
46 <mapping initial="none"> 47 <mapping initial="none">
47 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" /> 48 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
48 <add source="/" target="\/"/> 49 <add source="/" target="\/"/>
49 </mapping> 50 </mapping>
50
51 </sanitizer> 51 </sanitizer>
52 52 </param>
53 </param> 53 <param name="sed_options" type="text" size="20" optional="true" label="Additional sed commands before replacement" help="Provide additional sed commands before the replacement (e.g., ':a;N;$!ba;')." >
54 <sanitizer>
55 <valid initial="string.printable">
56 <remove value="&#39;"/> <!-- Removes single quotes -->
57 <remove value="/"/> <!-- Removes slashes -->
58 </valid>
59 <mapping initial="none">
60 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" /> <!-- Escapes single quotes -->
61 <add source="/" target="\/"/> <!-- Escapes slashes -->
62 </mapping>
63 </sanitizer>
64 </param>
54 </repeat> 65 </repeat>
55 </inputs> 66 </inputs>
56 <outputs> 67 <outputs>
57 <data name="outfile" format_source="infile" metadata_source="infile"/> 68 <data name="outfile" format_source="infile" metadata_source="infile"/>
58 </outputs> 69 </outputs>
59 <tests> 70 <tests>
60 <test> 71 <test>
61 <param name="infile" value="replace_text_in_line1.txt" /> 72 <param name="infile" value="replace_text_in_line1.txt" />
62 <param name="find_pattern" value="CTC." /> 73 <repeat name="replacements">
63 <param name="replace_pattern" value="FOOBAR" /> 74 <param name="find_pattern" value="CTC." />
75 <param name="replace_pattern" value="FOOBAR" />
76 <param name="sed_options" value="" />
77 </repeat>
64 <output name="outfile" file="replace_text_in_line_results1.txt" /> 78 <output name="outfile" file="replace_text_in_line_results1.txt" />
65 </test> 79 </test>
66 <test> 80 <test>
67 <param name="infile" value="replace_text_in_line1.txt" /> 81 <param name="infile" value="replace_text_in_line1.txt" />
68 <repeat name="replacements"> 82 <repeat name="replacements">
69 <param name="find_pattern" value="CTC." /> 83 <param name="find_pattern" value="CTC." />
70 <param name="replace_pattern" value="FOOBAR" /> 84 <param name="replace_pattern" value="FOOBAR" />
85 <param name="sed_options" value="" />
71 </repeat> 86 </repeat>
72 <repeat name="replacements"> 87 <repeat name="replacements">
73 <param name="find_pattern" value="chr" /> 88 <param name="find_pattern" value="chr" />
74 <param name="replace_pattern" value="domain" /> 89 <param name="replace_pattern" value="domain" />
90 <param name="sed_options" value="" />
75 </repeat> 91 </repeat>
76 <output name="outfile" file="replace_text_in_line_results2.txt" /> 92 <output name="outfile" file="replace_text_in_line_results2.txt" />
93 </test>
94 <test>
95 <param name="infile" value="replace_text_in_line1.txt" />
96 <repeat name="replacements">
97 <param name="find_pattern" value="\n" />
98 <param name="replace_pattern" value="" />
99 <param name="sed_options" value=":a;N;$!ba" />
100 </repeat>
101 <output name="outfile" file="replace_text_in_line_results3.txt" />
77 </test> 102 </test>
78 </tests> 103 </tests>
79 <help> 104 <help>
80 <![CDATA[ 105 <![CDATA[
81 **What it does** 106 **What it does**
153 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. 178 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
154 - **$** matches the end of a line or string. 179 - **$** matches the end of a line or string.
155 - **\|** Separates alternate possibilities. 180 - **\|** Separates alternate possibilities.
156 181
157 182
158 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. 183 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. However, you can use SED FAQ to perform commands using special characters.
184 More complex options can look like `sed -e '$!N;s/foo/bar/;'`. Here, `$!N;` is an optional part which you only need to set in very special cases. The `foo` part is the search string, and the `bar` part is the replacement string.
185 Please read the SED FAQ here: https://www.pement.org/sed/sedfaq3.html#s3.2
159 186
160 ]]> 187 ]]>
161 </help> 188 </help>
162 <expand macro="citations" /> 189 <expand macro="citations" />
163 </tool> 190 </tool>