<tool id="msconvert_subset" name="Subset Peak List" version="0.1.0">
  <description>against list of scan numbers or indices.</description>
  <command interpreter="python">
    msconvert_wrapper.py 
    --input=${input} 
    --output=${output} 
    --fromextension=${input.ext} 
    --toextension=${output_type} 
    #if $settings.settingsType == "full"
    --binaryencoding=${settings.binary_encoding} 
    --mzencoding=${settings.mz_encoding} 
    --intensityencoding=${settings.intensity_encoding}
    --zlib=${settings.zlib}
    #end if
    --filter_table="$filter.filterList"
    #if $filter.filterType == "scan_number"
    --filter_table_type="number"
    #else
    --filter_table_type="index"
    #end if
  </command>

  <inputs>
    <conditional name="type">
      <param name="input_type" type="select" label="Input Type">
        <option value="mzml">mzML</option>
        <option value="mzxml">mzXML</option>
        <option value="mgf">mgf</option>
        <option value="ms2">ms2</option>
      </param>
      <when value="mzml">
        <param format="mzml" name="input" type="data" label="Input mzML"/>
      </when>
      <when value="mzxml">
        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
      </when>
      <when value="mgf">
        <param format="mgf" name="input" type="data" label="Input mgf"/>
      </when>
      <when value="ms2">
        <param format="ms2" name="input" type="data" label="Input ms2"/>
      </when>
    </conditional>
    <param name="output_type" type="select" label="Output Type">
      <option value="mzML">mzML (indexed)</option>
      <option value="unindexed_mzML">mzML (unindexed)</option>
      <option value="mzXML">mzXML (indexed)</option>      
      <option value="unindexed_mzXML">mzXML (unindexed)</option>
      <option value="mgf">mgf</option>
      <option value="ms2">ms2</option>  
    </param>
    <conditional name="filter">
      <param name="filterType" type="select" label="Filter by" help="">
        <option value="scan_number" selected="true">Scan Number</option>
        <option value="scan_index">Scan Index</option>
      </param>    
      <when value="scan_number">
        <param format="text" name="filterList" type="data" label="Scan Numbers"/>
      </when>
      <when value="scan_index">
        <param format="text" name="filterList" type="data" label="Scan Indices"/>
      </when>
    </conditional>
    <conditional name="settings">
      <param name="settingsType" type="select" label="Advanced msconvert Settings" help="">
        <option value="default">Use Defaults</option>
        <option value="full">Full Parameter List</option>
      </param>
      <when value="default" />
      <when value="full">
        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
          <option value="64" selected="true">64</option>
          <option value="32">32</option>
        </param>
        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
          <option value="64" selected="true">64</option>
          <option value="32">32</option>
        </param>
        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
          <option value="64">64</option>
          <option value="32" selected="true">32</option>
        </param>
        <param type="boolean" name="zlib" label="Use zlib">      
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="mzml" name="output">
      <change_format>
        <when input="output_type" value="mzXML" format="mzxml" />
        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
        <when input="output_type" value="ms2" format="ms2" />
        <when input="output_type" value="mgf" format="mgf" />
      </change_format>
    </data>
  </outputs>

  <requirements>
    <requirement type="package">proteowizard</requirement>    
  </requirements>

  <help>
  </help>
</tool>