annotate changeCase.xml @ 1:3970d288ee1f draft

Updated command line format per dev team standards.

<tool id="ChangeCase" name="Change Case">
  <description> of selected columns</description>
  <stdio>
    <exit_code range="1:" err_level="fatal" />
  </stdio>
  <command interpreter="perl">changeCase.pl "${input}" "${cols}" "${delimiter}" "${casing}" "${out_file1}"</command>
  <inputs>
    <param name="input" format="txt" type="data" label="From"/>
    <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/>
    <param name="delimiter" type="select" label="Delimited by">
      <option value="TAB">Tab</option>
      <option value="SPACE">Whitespace</option>
      <option value="DOT">Dot</option>
      <option value="COMMA">Comma</option>
      <option value="DASH">Dash</option>
      <option value="UNDERSCORE">Underscore</option>
      <option value="PIPE">Pipe</option>
    </param>
    <param name="casing" type="select" label="To">
      <option value="up">Upper case</option>
      <option value="lo">Lower case</option>
    </param>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="1.txt" ftype="txt"/>
      <param name="cols" value="c1"/>
      <param name="delimiter" value="SPACE"/>
      <param name="casing" value="up"/>
      <output name="out_file1" file="changeCase_out1.tabular"/>
    </test>
    <test>
      <param name="input" value="1.bed" ftype="bed"/>
      <param name="cols" value="c1"/>
      <param name="delimiter" value="TAB"/>
      <param name="casing" value="up"/>
      <output name="out_file1" file="changeCase_out2.tabular"/>
    </test>
  </tests>
  <help>

.. class:: warningmark

**This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item.

.. class:: warningmark

The format of the resulting dataset from this tool is always tabular.

-----

**What it does**

This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case.

- Columns are specified as **c1**, **c2**, and so on.
- Columns can be specified in any order (e.g., **c2,c1,c6**)

-----

**Example**

Changing columns 1 and 3 ( delimited by Comma ) to upper case in::

  apple,is,good
  windows,is,bad

will result in::

  APPLE is GOOD
  WINDOWS is BAD

  </help>
</tool>