/
msconvert2.xml
23 lines (23 loc) · 1.23 KB
/
msconvert2.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
<?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="<class 'CTDopts.CTDopts._Null'>" 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>