Mercurial > repos > xuebing > sharplabtool
comparison tools/unix_tools/find_and_replace.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="cshl_find_and_replace" name="Find and Replace"> | |
2 <description>text</description> | |
3 <command interpreter="perl"> | |
4 find_and_replace.pl | |
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 | |
20 <!-- Note: the parameter ane MUST BE 'url_paste' - | |
21 This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142) | |
22 If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters | |
23 will be passed to the shell script --> | |
24 <param name="url_paste" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > | |
25 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> | |
26 </param> | |
27 | |
28 <param name="file_data" type="text" size="20" label="Replace with" help="Use simple text, or & (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." > | |
29 <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> | |
30 </param> | |
31 | |
32 <param name="is_regex" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Find-Pattern is a regular expression" | |
33 help="see help section for details." /> | |
34 | |
35 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" | |
36 help="" /> | |
37 | |
38 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" | |
39 help="ignore partial matches (e.g. 'apple' will not match 'snapple') " /> | |
40 | |
41 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" | |
42 help="Select this option if the first line contains column headers. Text in the line will not be replaced. " /> | |
43 | |
44 <conditional name="searchwhere"> | |
45 <param name="choice" type="select" label="Replace text in"> | |
46 <option value="line" selected="true">entire line</option> | |
47 <option value="column">specific column</option> | |
48 </param> | |
49 | |
50 <when value="line"> | |
51 </when> | |
52 | |
53 <when value="column"> | |
54 <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" /> | |
55 </when> | |
56 </conditional> | |
57 </inputs> | |
58 | |
59 <outputs> | |
60 <data format="input" name="output" metadata_source="input" /> | |
61 </outputs> | |
62 | |
63 <help> | |
64 | |
65 **What it does** | |
66 | |
67 This tool finds & replaces text in an input dataset. | |
68 | |
69 .. class:: infomark | |
70 | |
71 The **pattern to find** can be a simple text string, or a perl **regular expression** string (depending on *pattern is a regex* check-box). | |
72 | |
73 .. class:: infomark | |
74 | |
75 When using regular expressions, the **replace pattern** can contain back-references ( e.g. \\1 ) | |
76 | |
77 .. class:: infomark | |
78 | |
79 This tool uses Perl regular expression syntax. | |
80 | |
81 ----- | |
82 | |
83 **Examples of *regular-expression* Find Patterns** | |
84 | |
85 - **HELLO** The word 'HELLO' (case sensitive). | |
86 - **AG.T** The letters A,G followed by any single character, followed by the letter T. | |
87 - **A{4,}** Four or more consecutive A's. | |
88 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character. | |
89 - **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. | |
90 | |
91 | |
92 **Examples of Replace Patterns** | |
93 | |
94 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. | |
95 - **FOO-&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **&** (ampersand) represents the matched find pattern. | |
96 - **\\1** The text which matched the first parenthesis in the Find Pattern. | |
97 | |
98 | |
99 ----- | |
100 | |
101 **Example 1** | |
102 | |
103 **Find Pattern:** HELLO | |
104 **Replace Pattern:** WORLD | |
105 **Regular Expression:** no | |
106 **Replace what:** entire line | |
107 | |
108 Every time the word HELLO is found, it will be replaced with the word WORLD. | |
109 | |
110 ----- | |
111 | |
112 **Example 2** | |
113 | |
114 **Find Pattern:** ^chr | |
115 **Replace Pattern:** (empty) | |
116 **Regular Expression:** yes | |
117 **Replace what:** column 11 | |
118 | |
119 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" | |
120 | |
121 | |
122 ----- | |
123 | |
124 **Perl's Regular Expression Syntax** | |
125 | |
126 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. | |
127 | |
128 - **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. | |
129 - **^** matches the beginning of a string(but not an internal line). | |
130 - **(** .. **)** groups a particular pattern. | |
131 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. | |
132 | |
133 - **{n}** The preceding item is matched exactly n times. | |
134 - **{n,}** The preceding item ismatched n or more times. | |
135 - **{n,m}** The preceding item is matched at least n times but not more than m times. | |
136 | |
137 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**. | |
138 - **.** Matches any single character except a newline. | |
139 - ***** The preceding item will be matched zero or more times. | |
140 - **?** The preceding item is optional and matched at most once. | |
141 - **+** The preceding item will be matched one or more times. | |
142 - **^** has two meaning: | |
143 - matches the beginning of a line or string. | |
144 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. | |
145 - **$** matches the end of a line or string. | |
146 - **\\|** Separates alternate possibilities. | |
147 - **\\d** matches a single digit | |
148 - **\\w** matches a single letter or digit or an underscore. | |
149 - **\\s** matches a single white-space (space or tabs). | |
150 | |
151 | |
152 </help> | |
153 | |
154 </tool> |