comparison replace_text_in_line.xml @ 6:8928e6d1e7ba draft

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5:3f0e0d4c15a9

    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
    </expand>
    <version_command>sed --version | head -n 1</version_command>
    <command interpreter="sh">
<![CDATA[
        sed 
            -r
            --sandbox
            "s/$find_pattern/$replace_pattern/g"
            "$input"
        > "$output"
]]>
    </command>
    <inputs>
        <param format="txt" name="input" 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>

                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data format="input" name="output" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="replace_text_in_line_in1.txt" />
            <param name="find_pattern" value="CTC." />
            <param name="replace_pattern" value="FOOBAR" />
            <output name="output" file="replace_text_in_line_output1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool performs find &amp; replace operation on a specified file.

.. class:: infomark

The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').

**TIP:** If you need more complex patterns, use the *sed* tool.

-----


**Examples of Find Patterns**

- **HELLO**     The word 'HELLO' (case sensitive).
- **AG.T**      The letters A,G followed by any single character, followed by the letter T.
- **A{4,}**     Four or more consecutive A's.
- **chr2[012]\\t**       The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
- **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.



**Examples of Replace Patterns**

- **WORLD**  The word 'WORLD' will be placed whereever the find pattern was found.
- **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.
- **\\1**   The text which matched the first parenthesis in the Find Pattern.




-----

**Example 1**

-----

**Example 2**

**Find Pattern:** ^(.{4}) 
**Replace Pattern:** &\\t

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.


-----

6:8928e6d1e7ba

    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
    </expand>
    <version_command>sed --version | head -n 1</version_command>
    <command>
<![CDATA[
        sed 
            -r
            --sandbox
            "s/$find_pattern/$replace_pattern/g"
            "$infile"
        > "$outfile"
]]>
    </command>
    <inputs>
        <param format="txt" name="infile" 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>

                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <param name="find_pattern" value="CTC." />
            <param name="replace_pattern" value="FOOBAR" />
            <output name="outfile" file="replace_text_in_line_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool performs find & replace operation on a specified file.

.. class:: infomark

The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').

**TIP:** If you need more complex patterns, use the *sed* tool.

-----

**Examples of Find Patterns**

- **HELLO**     The word 'HELLO' (case sensitive).
- **AG.T**      The letters A,G followed by any single character, followed by the letter T.
- **A{4,}**     Four or more consecutive A's.
- **chr2[012]\\t**       The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
- **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.


**Examples of Replace Patterns**

- **WORLD**  The word 'WORLD' will be placed whereever the find pattern was found.
- **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.
- **\\1**   The text which matched the first parenthesis in the Find Pattern.


-----

**Example 1**

-----

**Example 2**

**Find Pattern:** ^(.{4}) 
**Replace Pattern:** &\\t

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.


-----