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comparison replace_text_in_line.xml @ 17:f2918761eaf3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f48156f03164bde1f1be4826b2f0a1f16dc2cd2f
author bgruening
date Tue, 20 Feb 2018 09:11:35 -0500
parents 61b3b01662fd
children 1e974b82380d
comparison
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16:61b3b01662fd 17:f2918761eaf3
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="ISO-8859-1"?>
2 <tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0"> 2 <tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0">
3 <description>in entire line</description> 3 <description>in entire line</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="4.2.3.dev0">sed</requirement> 8 <requirement type="package" version="4.2.3.dev0">sed</requirement>
9 </requirements> 9 </requirements>
10 <version_command>sed --version | head -n 1</version_command> 10 <version_command>sed --version | head -n 1</version_command>
11 <command> 11 <command>
12 <!--
13 This looks quite strange but it is intentional. We have used U+0090 as
14 the replacement brackets in the sed expression. This meets multiple requirements for use:
15
16 - is legal entity in XML 1.0 (https://en.wikipedia.org/wiki/Valid_characters_in_XML)
17 - is legal as a sed delimiter character (must be single-byte)
18 - is not in string.printable
19
20 Thus, this should execute properly. Additionally it allows users to
21 use characters like '/' and '\' and '|' in their regex without them
22 being able to prematurely terminate the expression.
23 -->
24 <![CDATA[ 12 <![CDATA[
25 sed 13 sed
26 -r 14 -r
27 --sandbox 15 --sandbox
28 's$find_pattern$replace_patterng' 16 's/$find_pattern/$replace_pattern/g'
29 '$infile' 17 '$infile'
30 > '$outfile' 18 > '$outfile'
31 ]]> 19 ]]>
20
32 </command> 21 </command>
33 <inputs> 22 <inputs>
34 <param format="txt" name="infile" type="data" label="File to process" /> 23 <param format="txt" name="infile" type="data" label="File to process" />
35 <param name="find_pattern" type="text" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 24 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
36 <sanitizer> 25 <sanitizer>
37 <valid initial="string.printable"> 26 <valid initial="string.printable">
38 <remove value="&apos;"/> 27 <remove value="&#39;"/>
28 <remove value="/"/>
39 </valid> 29 </valid>
30 <mapping initial="none">
31 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
32 <add source="/" target="\/"/>
33 </mapping>
40 </sanitizer> 34 </sanitizer>
41 </param> 35 </param>
42 <param name="replace_pattern" type="text" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > 36 <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." >
43 <sanitizer> 37 <sanitizer>
44 <valid initial="string.printable"> 38 <valid initial="string.printable">
45 <remove value="&apos;"/> 39 <remove value="&#39;"/>
40 <remove value="/"/>
46 </valid> 41 </valid>
42 <mapping initial="none">
43 <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
44 <add source="/" target="\/"/>
45 </mapping>
46
47 </sanitizer> 47 </sanitizer>
48
48 </param> 49 </param>
49 </inputs> 50 </inputs>
50 <outputs> 51 <outputs>
51 <data name="outfile" format_source="infile" metadata_source="infile"/> 52 <data name="outfile" format_source="infile" metadata_source="infile"/>
52 </outputs> 53 </outputs>
53 <tests> 54 <tests>
54 <test> 55 <test>
55 <param name="infile" value="replace_text_in_line1.txt" /> 56 <param name="infile" value="replace_text_in_line1.txt" />
56 <param name="find_pattern" value="CTC." /> 57 <param name="find_pattern" value="CTC." />
57 <param name="replace_pattern" value="FOOBAR" /> 58 <param name="replace_pattern" value="FOOBAR" />
58 <output name="outfile" file="replace_text_in_line_results1.txt" /> 59 <output name="outfile" file="replace_text_in_line_results1.txt" />
59 </test> 60 </test>
75 ----- 76 -----
76 77
77 **Examples of Find Patterns** 78 **Examples of Find Patterns**
78 79
79 - **HELLO** The word 'HELLO' (case sensitive). 80 - **HELLO** The word 'HELLO' (case sensitive).
80 - **AG.T** The letters A,G followed by any single character, followed by the letter T. 81 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
81 - **A{4,}** Four or more consecutive A's. 82 - **A{4,}** Four or more consecutive A's.
82 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. 83 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
83 - **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. 84 - **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.
84 85
85 86
86 **Examples of Replace Patterns** 87 **Examples of Replace Patterns**
87 88