comparison 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

26:f22a309187a3

<![CDATA[
   sed
      -r
      --sandbox
      #for $replacement in $replacements:
        -e
        's/$replacement.find_pattern/$replacement.replace_pattern/g'
      #end for
      '$infile'
      > '$outfile'

                </valid>
                <mapping initial="none">
                    <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                    <add source="/" target="\/"/>
                </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" />
            <param name="find_pattern" value="CTC." />
            <param name="replace_pattern" value="FOOBAR" />
            <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" />
            </repeat>
            <repeat name="replacements">
              <param name="find_pattern" value="chr" />
              <param name="replace_pattern" value="domain" />
            </repeat>
            <output name="outfile" file="replace_text_in_line_results2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

  - 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.

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

27:08cdbfffce67

<![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'

                </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**

  - 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>