annotate literal.xml @ 1:717a4009675c

literal.xml: adding custom color support

<tool id="visualdna" name="DNA visualizer" version="0.1">
  <description>Visualize DNA with colored pixels.</description>
  <command interpreter="python">literal.py $input -o $output -s ${width}x${height}
  #if $colors.custom:
    -A $AR,$AG,$AB -T $TR,$TG,$TB -G $GR,$GG,$GB -C $CR,$CG,$CB 
  #end if
  </command>
  <inputs>
    <param name="input" type="data" format="fasta" label="Input sequence" />
    <param name="width" type="integer" value="512" min="512" label="Output image width" help="in pixels" />
    <param name="height" type="integer" value="512" min="512" label="Output image height" help="in pixels" />
    <conditional name="colors">
      <param name="custom" type="select" label="Base colors">
        <option value="" selected="True">Use default colors</option>
        <option value="true">Use custom colors</option>
      </param>
      <when value="">
        <!-- do nothing -->
      </when>
      <when value="true">
        <!-- 'A':'0,255,0', 'T':'255,0,0', 'G':'255,255,255', 'C':'0,0,255' -->
        <param name="AR" type="integer" value="0" label="A red value" />
        <param name="AG" type="integer" value="255" label="A green value" />
        <param name="AB" type="integer" value="0" label="A blue value" />
        <param name="TR" type="integer" value="255" label="T red value" />
        <param name="TG" type="integer" value="0" label="T green value" />
        <param name="TB" type="integer" value="0" label="T blue value" />
        <param name="GR" type="integer" value="255" label="G red value" />
        <param name="GG" type="integer" value="255" label="G green value" />
        <param name="GB" type="integer" value="255" label="G blue value" />
        <param name="CR" type="integer" value="0" label="C red value" />
        <param name="CG" type="integer" value="0" label="C green value" />
        <param name="CB" type="integer" value="255" label="C blue value" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output" format="png"/>
  </outputs>
  <stdio>
    <exit_code range="1:" err_level="fatal"/>
    <exit_code range=":-1" err_level="fatal"/>
  </stdio>

  <help>

.. class:: infomark

**What it does**

This tool convert DNA sequence into a PNG image by representing each base with one colored pixel.

-----

.. class:: infomark

**Input Format**

The input sequence can be in FASTA format or a plain text file containing only the sequence. Any non-ATGC characters (case-insensitive) will be skipped.

  </help>

</tool>