ThermoRawFileParser

Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). It takes a thermo RAW file as input and outputs a metadata file and the spectra in 3 possible formats

  • MGF: only MS2 spectra
  • mzML and indexed mzML: both MS1 and MS2 spectra
  • Apache Parquet: under development

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved

(Linux) Requirements

Mono (install mono-complete if you encounter “assembly not found” errors).

Usage

mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0

For running on Windows, omit mono. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata -m=0|1 (0 for JSON, 1 for TXT) and the spectra file -f=0|1|2|3 (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet) or both. Use the -p flag to disable the thermo native peak peacking.

ThermoRawFileParser.exe --help
 usage is (use -option=value for the optional arguments):
  -h, --help                 Prints out the options.
  -i, --input=VALUE          The raw file input.
  -o, --output=VALUE         The output directory. Specify this or an output
                               file.
  -b, --output_file=VALUE    The output file. Specify this or an output
                               directory
  -f, --format=VALUE         The output format for the spectra (0 for MGF, 1
                               for mzMl, 2 for indexed mzML, 3 for Parquet)
  -m, --metadata=VALUE       The metadata output format (0 for JSON, 1 for TXT).
  -g, --gzip                 GZip the output file if this flag is specified (
                               without value).
  -p, --noPeakPicking        Don't use the peak picking provided by the native
                               thermo library (by default peak picking is
                               enabled)
  -v, --verbose              Enable verbose logging.
  -e, --ignoreInstrumentErrors
                             Ignore missing properties by the instrument.
  -u, --s3_url[=VALUE]       Optional property to write directly the data into
                               S3 Storage.
  -k, --s3_accesskeyid[=VALUE]
                             Optional key for the S3 bucket to write the file
                               output.
  -t, --s3_secretaccesskey[=VALUE]
                             Optional key for the S3 bucket to write the file
                               output.
  -n, --s3_bucketName[=VALUE]
                             S3 bucket name

Download

Click here to go to the release page.

Galaxy integration

ThermoRawFileParser is available in the Galaxy ToolShed and is deployed at the European Galaxy Server.

Build

If you want to build the project using nuget, put the ThermoFisher.CommonCore.RawFileReader.4.0.26.nupkg package in your local nuget directory.

Logging

The default log file is ThermoRawFileParser.log. The log settings can be changed in log4net.config.

Docker

Run ThermoRawFileParser simply with the pre-build biocontainer:

docker run -i -t -v /home/user/raw:/data_input quay.io/biocontainers/thermorawfileparser:1.1.2--0 ThermoRawFileParser.sh --help

Basic docker

Use the Dockerfile_basic docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser -f Dockerfile_basic .

Run example:

docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0

Create example for reusing the container:

docker create -v /home/user/raw:/data_input --name=rawparser -it thermorawparser
docker start rawparser
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/another_raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
docker stop rawparser

Biocontainers docker

Use the Dockerfile docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser .

Run example:

docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser mono /home/biodocker/bin/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0

or with the bash script (ThermoRawFileParser.sh):

docker run -v /home/user/raw:/data_input -i -t --user biodocker thermorawparser /bin/bash /home/biodocker/bin/ThermoRawFileParser.sh -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0