view convert_characters.xml @ 0:64d46676a13e draft

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<tool id="Convert characters1" name="Convert">
  <description>delimiters to TAB</description>
  <command interpreter="python">convert_characters.py $input $convert_from $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="Sp">Spaces</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>
    </param>
    <param format="txt" name="input" type="data" label="in Query"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="convert_from" value="s"/>
      <param name="input" value="1.bed"/>
      <output name="out_file1" file="eq-convert.dat"/>
    </test>
    <test>
      <param name="convert_from" value="s"/>
      <param name="input" value="a.txt"/>
      <output name="out_file1" file="a.tab"/>
    </test>
  </tests>
  <help>

**What it does**

Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.

-----

**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 TABs 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>