<tool id="idconvert" name="idconvert" version="@VERSION@.0">
    <description>Convert mass spectrometry identification files</description>

    <macros>
        <import>msconvert_macros.xml</import>
    </macros>

    <expand macro="generic_requirements" />

    <command>
<![CDATA[
#set input_name 
ln -s $input input.${input.extension}
idconvert input 

]]>
    </command>

    <inputs> 
        <conditional name="from">
            <param name="from_format" type="select" label="Convert from">
                <option value="mzid">mzIdentML (mzid)</option>
                <option value="protxml">protXML (protxml)</option>
                <option value="pepxml">pepXML (pepxml)</option>
            </param>
            <when value="mzid">
                <param name="input" type="data" format="pepxml,protxml,mzid" label="MS mzIdentML (mzid)" />
            </when>
            <when value="protxml">
                <param name="input" type="data" format="protxml" label="MS pepXML (pepxml)" />
                <param name="pepxml" type="data" format="pepxml" label="MS Identification" />
            </when>
            <when value="pepxml">
                <param name="input" type="data" format="pepxml" label="MS Identification" />
            </when>
        </conditional>
        <param name="to_format" type="select" label="Convert to">
            <option value="mzid">mzIdentML (mzid)</option>
            <option value="pepxml">pepXML (pepxml)</option>
            <option value="text">text</option>
        </param>
  </inputs>

  <tests>
  </tests>
  <help>
  </help>
  <expand macro="citations" />
</tool>