Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono. It takes a thermo RAW file as input and outputs a metadata file and the MS2 spectra (centroided) in MGF format.
RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved
The optional parameters only work in the -option=value format. The metadata file is only created when the -m is specified.
ThermoRawFileParser.exe usage (use -option=value for the optional arguments)
-h, --help Prints out the options.
-i, --input=VALUE The raw file input.
-o, --output=VALUE The metadata and mgf output directory.
-m, --metadata Write the metadata output file if this flag is
specified (without value).
-c, --collection[=VALUE] The optional collection identifier (PXD identifier
for example).
-r, --run[=VALUE] The optional mass spectrometry run name used in
the spectrum title. The RAW file name will be
used if not specified.
-s, --subfolder[=VALUE] Optional, to disambiguate instances where the same
collection has 2 or more MS runs with the same
name.
If you want to build the project using nuget, put the ThermoFisher.CommonCore.RawFileReader.4.0.26.nupkg package in your local nuget directory.
Use the docker file to build an image. It fetches to source code from github and builds it.
docker build -t thermorawparser .
Run example:
docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -m -c=PXD00001