<tool id="proteinpilot_tabular" version="0.1" name="ProteinPilot - Convert Group to Tabular">
  <description></description>
  <!-- TOOD: Implement wrapper allowing Windows newlines to be replaced. -->
  <command>
    #if $quant.use
    #set $denom = $quant.type
    #else
    #set $denom = ""
    #end if
    group2xml.exe ${type} $input $output $denom
  </command>
  <inputs>
    <param format="group" name="input" type="data" label="ProteinPilot Group Data" help=""/>
    <param name="type" type="select" label="Summary Type">
      <option value="PROTEIN">Protein</option>
      <option value="PEPTIDE">Peptide</option>
    </param>
    <conditional name="quant">
      <param name="use" type="boolean" label="Include quantation results" truevalue="true" falsevalue="false" />
      <when value="true">
        <param name="type" type="select" label="Denominator">
          <option value="IT113">113</option>
          <option value="IT114" selected="true">114</option>
          <option value="IT115">115</option>
          <option value="IT116">116</option>
          <option value="IT117">117</option>
          <option value="IT118">118</option>
          <option value="IT119">119</option>
          <option value="IT121">121</option>
          <option value="Light">Light</option>
          <option value="Heavy">Heavy</option>
          <option value="Medium">Medium</option>
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="${type} report for ${on_string}"/>
  </outputs>
  <help>
  </help>
</tool>