/tools/filters/grep.xml

 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
42The 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>