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comparison tools/filters/grep.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="Grep1" name="Select" version="1.0.1">
2 <description>lines that match an expression</description>
3 <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
4 <inputs>
5 <param format="txt" name="input" type="data" label="Select lines from"/>
6 <param name="invert" type="select" label="that">
7 <option value="false">Matching</option>
8 <option value="true">NOT Matching</option>
9 </param>
10 <param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
11 <sanitizer>
12 <valid initial="string.printable">
13 <remove value="&apos;"/>
14 </valid>
15 <mapping initial="none">
16 <add source="&apos;" target="__sq__"/>
17 </mapping>
18 </sanitizer>
19 </param>
20 </inputs>
21 <outputs>
22 <data format="input" name="out_file1" metadata_source="input"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="input" value="1.bed"/>
27 <param name="invert" value="false"/>
28 <param name="pattern" value="^chr[0-9]*"/>
29 <output name="out_file1" file="fs-grep.dat"/>
30 </test>
31 </tests>
32 <help>
33
34 .. class:: infomark
35
36 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
37
38 -----
39
40 **Syntax**
41
42 The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text.
43
44 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
45 - **\\A** matches the beginning of a string(but not an internal line).
46 - **\\d** matches a digit, same as [0-9].
47 - **\\D** matches a non-digit.
48 - **\\s** matches a whitespace character.
49 - **\\S** matches anything BUT a whitespace.
50 - **\\t** matches a tab.
51 - **\\w** matches an alphanumeric character.
52 - **\\W** matches anything but an alphanumeric character.
53 - **(** .. **)** groups a particular pattern.
54 - **\\Z** matches the end of a string(but not a internal line).
55 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
56
57 - **{n}** The preceding item is matched exactly n times.
58 - **{n,}** The preceding item is matched n or more times.
59 - **{n,m}** The preceding item is matched at least n times but not more than m times.
60
61 - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
62 - **.** Matches any single character except a newline.
63 - ***** The preceding item will be matched zero or more times.
64 - **?** The preceding item is optional and matched at most once.
65 - **+** The preceding item will be matched one or more times.
66 - **^** has two meaning:
67 - matches the beginning of a line or string.
68 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
69 - **$** matches the end of a line or string.
70 - **\|** Separates alternate possibilities.
71
72 -----
73
74 **Example**
75
76 - **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file.
77 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
78 - **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651.
79 - **(abc)|(def)** would match either "abc" or "def".
80 - **^\\W+#** would match any line that is a comment.
81 </help>
82 </tool>