annotate msconvert_win.xml @ 0:f8cf3be564bb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty

<tool id="msconvert_win" name="msconvert (vendor support)" version="@VERSION@.0">
  <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description>

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

  <expand macro="msconvertCommand" />

  <inputs>
    <!-- TODO: add Bruker, Waters, Agilent types -->
    <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" />

    <expand macro="msconvertInputParameters" />
  </inputs>

  <expand macro="msconvertOutput" />

  <tests>
    <expand macro="msconvert_tests" />

    <test>
      <param name="input" value="small.raw" />
      <param name="output_type" value="mgf" />
      <param name="pick_peaks" value="true" />
      <param name="pick_peaks_algorithm" value="vendor" />
      <param name="pick_peaks_ms_levels" value="1" />
      <output name="output" file="small-peakpicking-vendor-ms1.mgf" />
    </test>

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