comparison find_and_replace.xml @ 7:d64eace4f9f3 draft

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6:8928e6d1e7ba

            '$infile'
]]>
    </command>
    <inputs>
        <param name="infile" format="txt" type="data" label="File to process" />
        <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " > 
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>

-----

**Example 2**

**Find Pattern:** ^chr 
**Replace Pattern:** (empty)
**Regular Expression:** yes
**Replace what:** column 11

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"

-----

**Perl's Regular Expression Syntax**

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. 

- **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).
- **(** .. **)** groups a particular pattern.
- **{** 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 ismatched 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. 
- **\\d** matches a single digit
- **\\w** matches a single letter or digit or an underscore.
- **\\s** matches a single white-space (space or tabs).

@REFERENCES@

7:d64eace4f9f3

            '$infile'
]]>
    </command>
    <inputs>
        <param name="infile" format="txt" type="data" label="File to process" />
        <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>

-----

**Example 2**

**Find Pattern:** ^chr
**Replace Pattern:** (empty)
**Regular Expression:** yes
**Replace what:** column 11

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"

-----

**Perl's Regular Expression Syntax**

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.

- **( ) { } [ ] . * ? + \\ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
- **^** matches the beginning of a string(but not an internal line).
- **(** .. **)** groups a particular pattern.
- **{** 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 ismatched 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.
- **\\d** matches a single digit
- **\\w** matches a single letter or digit or an underscore.
- **\\s** matches a single white-space (space or tabs).

@REFERENCES@