library and command line tool to convert Thermo Fisher raw files to mz(X)ML
raw2mzml is a Python package for wraping common use cases of msconvert.exe commandline tool.
msconvert.exe is part of Proteowizard (<http://proteowizard.sourceforge.net/>) and allows conversion from Thermo Fisher .raw files to open source formats .mzML and .mzXML. It has many options and getting them right is not always easy and wrong usage results in wrong conversion results. Instead raw2mzml has only a configurable options which cover common use cases.
Beyond the package it ships with a command line tool having the same name. After installation you might run
$ raw2mzml –help
to learn about its usage.