Mercurial > repos > bgruening > text_processing

annotate replace_text_in_line.xml @ 23:6073bb457ec0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 7cdafed6c6a1387395e5a869186518f129aa3132
author bgruening
date Tue, 25 Mar 2025 14:34:17 +0000
parents 3dc70b59608c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 12
diff changeset
1 <tool id="tp_replace_in_line" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
2 <description>in entire line</description>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
3 <macros>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
4 <import>macros.xml</import>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
5 </macros>
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 12
diff changeset
6 <expand macro="creator"/>
5
20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
parents: 3
diff changeset
7 <requirements>
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 12
diff changeset
8 <requirement type="package" version="4.8">sed</requirement>
5
20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
parents: 3
diff changeset
9 </requirements>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
10 <version_command>sed --version | head -n 1</version_command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
11 <command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
12 <![CDATA[
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
13 sed
11
74a8bef53a00 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
bgruening
parents: 10
diff changeset
14 -r
74a8bef53a00 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
bgruening
parents: 10
diff changeset
15 --sandbox
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
16 #for $replacement in $replacements:
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
17 -e '$replacement.sed_options'
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
18 -e
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
19 's/$replacement.find_pattern/$replacement.replace_pattern/g'
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
20 #end for
11
74a8bef53a00 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
bgruening
parents: 10
diff changeset
21 '$infile'
74a8bef53a00 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7
bgruening
parents: 10
diff changeset
22 > '$outfile'
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
23 ]]>
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
24
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
25 </command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
26 <inputs>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
27 <param format="txt" name="infile" type="data" label="File to process" />
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
28 <repeat name="replacements" title="Replacement" min="1">
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
29 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
30 <sanitizer>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
31 <valid initial="string.printable">
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
32 <remove value="&#39;"/>
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
33 <remove value="/"/>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
34 </valid>
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
35 <mapping initial="none">
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
36 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
37 <add source="/" target="\/"/>
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
38 </mapping>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
39 </sanitizer>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
40 </param>
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
41 <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
42 <sanitizer>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
43 <valid initial="string.printable">
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
44 <remove value="&#39;"/>
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
45 <remove value="/"/>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
46 </valid>
10
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
47 <mapping initial="none">
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
48 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
49 <add source="/" target="\/"/>
e39fceb6ab85 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
bgruening
parents: 9
diff changeset
50 </mapping>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
51 </sanitizer>
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
52 </param>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
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;')." >
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
54 <sanitizer>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
55 <valid initial="string.printable">
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
56 <remove value="&#39;"/> <!-- Removes single quotes -->
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
57 <remove value="/"/> <!-- Removes slashes -->
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
58 </valid>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
59 <mapping initial="none">
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
60 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" /> <!-- Escapes single quotes -->
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
61 <add source="/" target="\/"/> <!-- Escapes slashes -->
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
62 </mapping>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
63 </sanitizer>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
64 </param>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
65 </repeat>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
66 </inputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
67 <outputs>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
68 <data name="outfile" format_source="infile" metadata_source="infile"/>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
69 </outputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
70 <tests>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
71 <test>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
72 <param name="infile" value="replace_text_in_line1.txt" />
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
73 <repeat name="replacements">
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
74 <param name="find_pattern" value="CTC." />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
75 <param name="replace_pattern" value="FOOBAR" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
76 <param name="sed_options" value="" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
77 </repeat>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
78 <output name="outfile" file="replace_text_in_line_results1.txt" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
79 </test>
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
80 <test>
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
81 <param name="infile" value="replace_text_in_line1.txt" />
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
82 <repeat name="replacements">
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
83 <param name="find_pattern" value="CTC." />
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
84 <param name="replace_pattern" value="FOOBAR" />
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
85 <param name="sed_options" value="" />
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
86 </repeat>
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
87 <repeat name="replacements">
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
88 <param name="find_pattern" value="chr" />
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
89 <param name="replace_pattern" value="domain" />
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
90 <param name="sed_options" value="" />
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
91 </repeat>
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
92 <output name="outfile" file="replace_text_in_line_results2.txt" />
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
93 </test>
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
94 <test>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
95 <param name="infile" value="replace_text_in_line1.txt" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
96 <repeat name="replacements">
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
97 <param name="find_pattern" value="\n" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
98 <param name="replace_pattern" value="" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
99 <param name="sed_options" value=":a;N;$!ba" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
100 </repeat>
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
101 <output name="outfile" file="replace_text_in_line_results3.txt" />
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
102 </test>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
103 </tests>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
104 <help>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
105 <![CDATA[
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
106 **What it does**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
107
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
108 This tool performs find & replace operation on a specified file.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
109
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
110 .. class:: infomark
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
111
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
112 The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
113
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
114 .. class:: infomark
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
115
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
116 **TIP:** If you need more complex patterns, use the *sed* tool.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
117
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
118 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
119
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
120 **Examples of Find Patterns**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
121
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
122 - **HELLO** The word 'HELLO' (case sensitive).
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
123 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
124 - **A{4,}** Four or more consecutive A's.
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
125 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
126 - **hsa-mir-([^ ]+)** The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
127
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
128
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
129 **Examples of Replace Patterns**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
130
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
131 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
6
60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents: 5
diff changeset
132 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the beginning and '-BAR' at the end. **&** (ampersand) represents the matched find pattern.
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
133 - **\\1** The text which matched the first parenthesis in the Find Pattern.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
134
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
135
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
136 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
137
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
138 **Example 1**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
139
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
140 **Find Pattern:** HELLO
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
141 **Replace Pattern:** WORLD
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
142
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
143 Every time the word HELLO is found, it will be replaced with the word WORLD.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
144
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
145
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
146 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
147
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
148 **Example 2**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
149
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
150 **Find Pattern:** ^(.{4})
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
151 **Replace Pattern:** &\\t
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
152
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
153 Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
154
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
155
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
156 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
157
12
a6f147a050a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8
bgruening
parents: 11
diff changeset
158 **Extended Regular Expression Syntax**
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
159
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
160 The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
161
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
162 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
163 - **^** matches the beginning of a string(but not an internal line).
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
164 - **(** .. **)** groups a particular pattern.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
165 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
166
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
167 - **{n}** The preceding item is matched exactly n times.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
168 - **{n,}** The preceding item ismatched n or more times.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
169 - **{n,m}** The preceding item is matched at least n times but not more than m times.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
170
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
171 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
172 - **.** Matches any single character except a newline.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
173 - ***** The preceding item will be matched zero or more times.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
174 - **?** The preceding item is optional and matched at most once.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
175 - **+** The preceding item will be matched one or more times.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
176 - **^** has two meaning:
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
177 - matches the beginning of a line or string.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
178 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
179 - **$** matches the end of a line or string.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
180 - **\|** Separates alternate possibilities.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
181
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
182
22
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
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.
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
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.
3dc70b59608c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b
bgruening
parents: 19
diff changeset
185 Please read the SED FAQ here: https://www.pement.org/sed/sedfaq3.html#s3.2
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
186
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
187 ]]>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
188 </help>
6
60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents: 5
diff changeset
189 <expand macro="citations" />
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
190 </tool>