Mercurial > repos > bgruening > text_processing
comparison find_and_replace.xml @ 0:ec66f9d90ef0 draft
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author | bgruening |
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date | Thu, 05 Sep 2013 04:58:21 -0400 |
parents | |
children | a4ad586d1403 |
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1 <tool id="cshl_find_and_replace" name="Find and Replace" version="0.1.1"> | |
2 <description>text</description> | |
3 <command interpreter="perl"> | |
4 find_and_replace | |
5 #if $searchwhere.choice == "column": | |
6 -c $searchwhere.column | |
7 #end if | |
8 -o $output | |
9 $caseinsensitive | |
10 $wholewords | |
11 $skip_first_line | |
12 $is_regex | |
13 '$url_paste' | |
14 '$file_data' | |
15 '$input' | |
16 </command> | |
17 <inputs> | |
18 <param format="txt" name="input" type="data" label="File to process" /> | |
19 <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > | |
20 <sanitizer> | |
21 <valid initial="string.printable"> | |
22 <remove value="'"/> | |
23 </valid> | |
24 </sanitizer> | |
25 </param> | |
26 | |
27 <param name="file_data" type="text" size="20" label="Replace with" help="Use simple text, or $& (dollar-ampersand) and $1 $2 $3 to refer to matched text. See examples below." > | |
28 <sanitizer> | |
29 <valid initial="string.printable"> | |
30 <remove value="'"/> | |
31 </valid> | |
32 </sanitizer> | |
33 </param> | |
34 | |
35 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression" | |
36 help="see help section for details." /> | |
37 | |
38 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" | |
39 help="" /> | |
40 | |
41 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" | |
42 help="ignore partial matches (e.g. 'apple' will not match 'snapple') " /> | |
43 | |
44 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" | |
45 help="Select this option if the first line contains column headers. Text in the line will not be replaced. " /> | |
46 | |
47 <conditional name="searchwhere"> | |
48 <param name="choice" type="select" label="Replace text in"> | |
49 <option value="line" selected="true">entire line</option> | |
50 <option value="column">specific column</option> | |
51 </param> | |
52 <when value="line" /> | |
53 | |
54 <when value="column"> | |
55 <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" /> | |
56 </when> | |
57 </conditional> | |
58 </inputs> | |
59 | |
60 <outputs> | |
61 <data format="input" name="output" metadata_source="input" /> | |
62 </outputs> | |
63 | |
64 <help> | |
65 | |
66 **What it does** | |
67 | |
68 This tool finds & replaces text in an input dataset. | |
69 | |
70 .. class:: infomark | |
71 | |
72 The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box). | |
73 | |
74 .. class:: infomark | |
75 | |
76 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 ) | |
77 | |
78 .. class:: infomark | |
79 | |
80 This tool uses Perl regular expression syntax. | |
81 | |
82 ----- | |
83 | |
84 **Examples of *regular-expression* Find Patterns** | |
85 | |
86 - **HELLO** The word 'HELLO' (case sensitive). | |
87 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
88 - **A{4,}** Four or more consecutive A's. | |
89 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
90 - **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. | |
91 | |
92 | |
93 **Examples of Replace Patterns** | |
94 | |
95 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
96 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern. | |
97 - **$1** The text which matched the first parenthesis in the Find Pattern. | |
98 | |
99 | |
100 ----- | |
101 | |
102 **Example 1** | |
103 | |
104 **Find Pattern:** HELLO | |
105 **Replace Pattern:** WORLD | |
106 **Regular Expression:** no | |
107 **Replace what:** entire line | |
108 | |
109 Every time the word HELLO is found, it will be replaced with the word WORLD. | |
110 | |
111 ----- | |
112 | |
113 **Example 2** | |
114 | |
115 **Find Pattern:** ^chr | |
116 **Replace Pattern:** (empty) | |
117 **Regular Expression:** yes | |
118 **Replace what:** column 11 | |
119 | |
120 If column 11 (of every line) begins with ther letters 'chr', they will be removed. Effectively, it'll turn "chr4" into "4" and "chrXHet" into "XHet" | |
121 | |
122 | |
123 ----- | |
124 | |
125 **Perl's Regular Expression Syntax** | |
126 | |
127 The Find & Replace 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. | |
128 | |
129 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
130 - **^** matches the beginning of a string(but not an internal line). | |
131 - **(** .. **)** groups a particular pattern. | |
132 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
133 | |
134 - **{n}** The preceding item is matched exactly n times. | |
135 - **{n,}** The preceding item ismatched n or more times. | |
136 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
137 | |
138 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
139 - **.** Matches any single character except a newline. | |
140 - ***** The preceding item will be matched zero or more times. | |
141 - **?** The preceding item is optional and matched at most once. | |
142 - **+** The preceding item will be matched one or more times. | |
143 - **^** has two meaning: | |
144 - matches the beginning of a line or string. | |
145 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. | |
146 - **$** matches the end of a line or string. | |
147 - **\\|** Separates alternate possibilities. | |
148 - **\\d** matches a single digit | |
149 - **\\w** matches a single letter or digit or an underscore. | |
150 - **\\s** matches a single white-space (space or tabs). | |
151 | |
152 | |
153 </help> | |
154 | |
155 </tool> |