msconvert.xml

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [File Handling]-->
<tool id="msconvert" name="msconvert" version="3.0.9098-0.2">
  <requirements>
    <container type="docker">phnmnl/pwiz</container>
  </requirements>
  <description>Converts vendor RAW MS to mzML.</description>
  <command>
    wine "/home/xclient/.wine/drive_c/Program Files/ProteoWizard/ProteoWizard/msconvert.exe" $infile  2>/dev/null | cat >$outfile
</command>
  <inputs>
    <param name="param_REMAININGPARAMETERS" type="data" format="" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="Input file(s) to convert" help="(-REMAININGPARAMETERS) "/>
  </inputs>
  <outputs>
    <data name="outfile" format="data"/>
  </outputs>
  <help>Converts between different MS file formats. For more information, visit http://proteowizard.sourceforge.net/tools/msconvert.html</help>
</tool>