/tools/filters/grep.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 82 lines · 71 code · 11 blank · 0 comment · 0 complexity · 2891f6dc7c9c27dd7cef3c124eaeceeb MD5 · raw file
- <tool id="Grep1" name="Select" version="1.0.1">
- <description>lines that match an expression</description>
- <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
- <inputs>
- <param format="txt" name="input" type="data" label="Select lines from"/>
- <param name="invert" type="select" label="that">
- <option value="false">Matching</option>
- <option value="true">NOT Matching</option>
- </param>
- <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)">
- <sanitizer>
- <valid initial="string.printable">
- <remove value="'"/>
- </valid>
- <mapping initial="none">
- <add source="'" target="__sq__"/>
- </mapping>
- </sanitizer>
- </param>
- </inputs>
- <outputs>
- <data format="input" name="out_file1" metadata_source="input"/>
- </outputs>
- <tests>
- <test>
- <param name="input" value="1.bed"/>
- <param name="invert" value="false"/>
- <param name="pattern" value="^chr[0-9]*"/>
- <output name="out_file1" file="fs-grep.dat"/>
- </test>
- </tests>
- <help>
- .. class:: infomark
- **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
- -----
- **Syntax**
- 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.
- - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- - **\\A** matches the beginning of a string(but not an internal line).
- - **\\d** matches a digit, same as [0-9].
- - **\\D** matches a non-digit.
- - **\\s** matches a whitespace character.
- - **\\S** matches anything BUT a whitespace.
- - **\\t** matches a tab.
- - **\\w** matches an alphanumeric character.
- - **\\W** matches anything but an alphanumeric character.
- - **(** .. **)** groups a particular pattern.
- - **\\Z** matches the end of a string(but not a internal line).
- - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
- - **{n}** The preceding item is matched exactly n times.
- - **{n,}** The preceding item is matched n or more times.
- - **{n,m}** The preceding item is matched at least n times but not more than m times.
- - **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
- - **.** Matches any single character except a newline.
- - ***** The preceding item will be matched zero or more times.
- - **?** The preceding item is optional and matched at most once.
- - **+** The preceding item will be matched one or more times.
- - **^** has two meaning:
- - matches the beginning of a line or string.
- - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
- - **$** matches the end of a line or string.
- - **\|** Separates alternate possibilities.
- -----
- **Example**
- - **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file.
- - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
- - **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651.
- - **(abc)|(def)** would match either "abc" or "def".
- - **^\\W+#** would match any line that is a comment.
- </help>
- </tool>