ExternalTools

OpenMS supports the wrapping of external tools (like msconvert from ProteoWizard?), thus allowing you to build TOPPAS pipelines containing external tools.

How to add and use external tools is described in a ReadMe.txt shipped with OpenMS https://sourceforge.net/apps/trac/open-ms/browser/OpenMS/share/OpenMS/TOOLS/EXTERNAL/ReadMe.txt?format=txt