|
4
|
1 <tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0">
|
|
3
|
2 <description>in entire line</description>
|
|
4
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements">
|
|
3
|
7 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
|
|
4
|
8 </expand>
|
|
|
9 <version_command>sed --version | head -n 1</version_command>
|
|
3
|
10 <command interpreter="sh">
|
|
4
|
11 <![CDATA[
|
|
|
12 sed
|
|
|
13 -r
|
|
|
14 --sandbox
|
|
|
15 "s/$find_pattern/$replace_pattern/g"
|
|
|
16 "$input"
|
|
|
17 > "$output"
|
|
|
18 ]]>
|
|
3
|
19 </command>
|
|
|
20 <inputs>
|
|
|
21 <param format="txt" name="input" type="data" label="File to process" />
|
|
|
22 <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
|
|
|
23 <sanitizer>
|
|
|
24 <valid initial="string.printable">
|
|
|
25 <remove value="'"/>
|
|
|
26 </valid>
|
|
|
27 </sanitizer>
|
|
|
28 </param>
|
|
|
29 <param name="replace_pattern" 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." >
|
|
|
30 <sanitizer>
|
|
|
31 <valid initial="string.printable">
|
|
|
32 <remove value="'"/>
|
|
|
33 </valid>
|
|
|
34 </sanitizer>
|
|
|
35 </param>
|
|
|
36 </inputs>
|
|
|
37 <outputs>
|
|
|
38 <data format="input" name="output" metadata_source="input"/>
|
|
|
39 </outputs>
|
|
4
|
40 <tests>
|
|
|
41 <test>
|
|
|
42 <param name="input" value="replace_text_in_line_in1.txt" />
|
|
|
43 <param name="find_pattern" value="CTC." />
|
|
|
44 <param name="replace_pattern" value="FOOBAR" />
|
|
|
45 <output name="output" file="replace_text_in_line_output1.txt" />
|
|
|
46 </test>
|
|
|
47 </tests>
|
|
3
|
48 <help>
|
|
4
|
49 <![CDATA[
|
|
3
|
50 **What it does**
|
|
|
51
|
|
|
52 This tool performs find & replace operation on a specified file.
|
|
|
53
|
|
|
54 .. class:: infomark
|
|
|
55
|
|
|
56 The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').
|
|
|
57
|
|
|
58 .. class:: infomark
|
|
|
59
|
|
|
60 **TIP:** If you need more complex patterns, use the *sed* tool.
|
|
|
61
|
|
|
62 -----
|
|
|
63
|
|
|
64
|
|
|
65 **Examples of Find Patterns**
|
|
|
66
|
|
|
67 - **HELLO** The word 'HELLO' (case sensitive).
|
|
|
68 - **AG.T** The letters A,G followed by any single character, followed by the letter T.
|
|
|
69 - **A{4,}** Four or more consecutive A's.
|
|
|
70 - **chr2[012]\\t** The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
|
|
|
71 - **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.
|
|
|
72
|
|
|
73
|
|
|
74
|
|
|
75 **Examples of Replace Patterns**
|
|
|
76
|
|
|
77 - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found.
|
|
|
78 - **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.
|
|
|
79 - **\\1** The text which matched the first parenthesis in the Find Pattern.
|
|
|
80
|
|
|
81
|
|
|
82
|
|
|
83
|
|
|
84 -----
|
|
|
85
|
|
|
86 **Example 1**
|
|
|
87
|
|
|
88 **Find Pattern:** HELLO
|
|
|
89 **Replace Pattern:** WORLD
|
|
|
90
|
|
|
91 Every time the word HELLO is found, it will be replaced with the word WORLD.
|
|
|
92
|
|
|
93
|
|
|
94 -----
|
|
|
95
|
|
|
96 **Example 2**
|
|
|
97
|
|
|
98 **Find Pattern:** ^(.{4})
|
|
|
99 **Replace Pattern:** &\\t
|
|
|
100
|
|
|
101 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.
|
|
|
102
|
|
|
103
|
|
|
104 -----
|
|
|
105
|
|
|
106 **Extened Regular Expression Syntax**
|
|
|
107
|
|
|
108 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.
|
|
|
109
|
|
|
110 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
|
|
|
111 - **^** matches the beginning of a string(but not an internal line).
|
|
|
112 - **(** .. **)** groups a particular pattern.
|
|
|
113 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
|
|
|
114
|
|
|
115 - **{n}** The preceding item is matched exactly n times.
|
|
|
116 - **{n,}** The preceding item ismatched n or more times.
|
|
|
117 - **{n,m}** The preceding item is matched at least n times but not more than m times.
|
|
|
118
|
|
|
119 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
|
|
|
120 - **.** Matches any single character except a newline.
|
|
|
121 - ***** The preceding item will be matched zero or more times.
|
|
|
122 - **?** The preceding item is optional and matched at most once.
|
|
|
123 - **+** The preceding item will be matched one or more times.
|
|
|
124 - **^** has two meaning:
|
|
|
125 - matches the beginning of a line or string.
|
|
|
126 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
|
|
|
127 - **$** matches the end of a line or string.
|
|
|
128 - **\|** Separates alternate possibilities.
|
|
|
129
|
|
|
130
|
|
|
131 **Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
|
|
|
132
|
|
4
|
133 @REFERENCES@
|
|
|
134 ]]>
|
|
3
|
135 </help>
|
|
|
136 </tool>
|
