view replace_delimiter/replace_delimiter.xml @ 0:295395b4b28f draft default tip

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<tool id="convertdelimiter" name="Convert">
  <description>delimiters</description>
  <command interpreter="python">replace_delimiter.py $input $convert_from $convert_to $out_file1</command>
  <inputs>
    <param name="convert_from" type="select" label="Convert all">
      <option value="s">Whitespaces</option>
      <option value="T">Tabs</option>
      <option value="Dt">Dots</option>
      <option value="C">Commas</option>
      <option value="D">Dashes</option>
      <option value="U">Underscores</option>
      <option value="P">Pipes</option>
      <option value="Co">Colons</option>
      <option value="Sc">Semicolons</option>
    </param>
    <param format="txt" name="input" type="data" label="in Dataset"/>
    <param name="convert_to" type="select" label="to ">
      <option value="s">Whitespaces</option>
      <option value="T">Tabs</option>
      <option value="Dt">Dots</option>
      <option value="C">Commas</option>
      <option value="D">Dashes</option>
      <option value="U">Underscores</option>
      <option value="P">Pipes</option>
      <option value="Co">Colons</option>
      <option value="Sc">Semicolons</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="convert_from" value="P"/>
      <param name="input" value="replace_delimiter_input.tsv" ftype="tabular"/>
      <param name="convert_to" value="C"/>
      <output name="out_file1" file="replace_delimiter_output.csv"/>
    </test>
  </tests>
  <help>

**What it does**

Converts all delimiters of a specified type into a specified delimiter(Dots, Commas, Dashes, Underscores, Pipes, Colons, Semicolons).
Tool and code borrowed from convert_delimiter tool(distributed with Galaxy).
-----

**Example**

- Input file:

    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+

- Converting all pipe delimiters of the above file to Commas will get::

    chrX,151283558,151283724,NM_000808_exon_8_0_chrX_151283559_r,0,-
    chrX,151370273,151370486,NM_000808_exon_9_0_chrX_151370274_r,0,-
    chrX,151559494,151559583,NM_018558_exon_1_0_chrX_151559495_f,0,+
    chrX,151564643,151564711,NM_018558_exon_2_0_chrX_151564644_f,0,+

</help>
</tool>