msconvert2.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="msconvert2" name="msconvert2" version="3.0.9098-2.2">
  <requirements>
    <container type="docker">phnmnl/pwiz</container>
  </requirements>
  <description>Converts vendor RAW MS to mzML.</description>
  <command><![CDATA[
    mkdir -p \$PWD/tmp_msconvert/out;
    unzip -q -d \$PWD/tmp_msconvert/out $infile;
    chown -R xclient:xusers \$PWD/tmp_msconvert;
    su xclient -c "wine '/home/xclient/.wine/drive_c/Program Files/ProteoWizard/ProteoWizard/msconvert.exe' \$PWD/tmp_msconvert/out --mzML -o \$PWD/tmp_msconvert" 2>/dev/null;
    sudo mv \$PWD/tmp_msconvert/out.mzML $outfile
  ]]></command>
  <inputs>
    <param name="infile" type="data" format="data" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" optional="False" label="Input file to convert" />
  </inputs>
  <outputs>
    <data name="outfile" type="data" format="mzml"/>
  </outputs>
  <help>Converts between different MS file formats. For more information, visit http://proteowizard.sourceforge.net/tools/msconvert.html</help>
</tool>