view replace_text_in_line.xml @ 27:08cdbfffce67 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b

<tool id="tp_replace_in_line" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>in entire line</description>
    <macros>
       <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="4.8">sed</requirement>
    </requirements>
    <version_command>sed --version | head -n 1</version_command>
    <command>
<![CDATA[
   sed
      -r
      --sandbox
      #for $replacement in $replacements:
        -e '$replacement.sed_options'
        -e
        's/$replacement.find_pattern/$replacement.replace_pattern/g'
      #end for
      '$infile'
      > '$outfile'
]]>

    </command>
    <inputs>
      <param format="txt" name="infile" type="data" label="File to process" />
      <repeat name="replacements" title="Replacement" min="1">
         <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="&#39;"/>
                    <remove value="/"/>
                </valid>
                <mapping initial="none">
                    <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                    <add source="/" target="\/"/>
                </mapping>
            </sanitizer>
         </param>
         <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&#39;"/>
                    <remove value="/"/>
                </valid>
                <mapping initial="none">
                    <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                    <add source="/" target="\/"/>
                </mapping>
            </sanitizer>
         </param>
         <param name="sed_options" type="text" size="20" optional="true" label="Additional sed commands before replacement" help="Provide additional sed commands before the replacement (e.g., ':a;N;$!ba;')." >
            <sanitizer>
              <valid initial="string.printable">
                  <remove value="&#39;"/>  <!-- Removes single quotes -->
                  <remove value="/"/>     <!-- Removes slashes -->
              </valid>
              <mapping initial="none">
                  <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />  <!-- Escapes single quotes -->
                  <add source="/" target="\/"/>                         <!-- Escapes slashes -->
              </mapping>
            </sanitizer>
         </param>
      </repeat>
    </inputs>
    <outputs>
  <data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
         <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <repeat name="replacements">
              <param name="find_pattern" value="CTC." />
              <param name="replace_pattern" value="FOOBAR" />
              <param name="sed_options" value="" />
            </repeat>
            <output name="outfile" file="replace_text_in_line_results1.txt" />
        </test>
        <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <repeat name="replacements">
              <param name="find_pattern" value="CTC." />
              <param name="replace_pattern" value="FOOBAR" />
              <param name="sed_options" value="" />
            </repeat>
            <repeat name="replacements">
              <param name="find_pattern" value="chr" />
              <param name="replace_pattern" value="domain" />
              <param name="sed_options" value="" />
            </repeat>
            <output name="outfile" file="replace_text_in_line_results2.txt" />
        </test>
        <test>
            <param name="infile" value="replace_text_in_line1.txt" />
            <repeat name="replacements">
            <param name="find_pattern" value="\n" />
            <param name="replace_pattern" value="" />
            <param name="sed_options" value=":a;N;$!ba" />
            </repeat>
            <output name="outfile" file="replace_text_in_line_results3.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').

.. class:: infomark

**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 beginning 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**

**Find Pattern:** HELLO
**Replace Pattern:** WORLD

Every time the word HELLO is found, it will be replaced with the word WORLD.


-----

**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.


-----

**Extended Regular Expression Syntax**

The select 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.


**Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. However, you can use SED FAQ to perform commands using special characters.
        More complex options can look like `sed -e '$!N;s/foo/bar/;'`. Here, `$!N;` is an optional part which you only need to set in very special cases. The `foo` part is the search string, and the `bar` part is the replacement string.
        Please read the SED FAQ here: https://www.pement.org/sed/sedfaq3.html#s3.2

]]>
    </help>
    <expand macro="citations" />
</tool>