msconvert-cli

Python CLI wrapper for ProteoWizard's MS-Convert that runs in Docker containers. Convert mass spectrometry files (.raw, .wiff, .d, etc.) to mzML/MGF/... formats with parallel processing.

Installation

pip install msconvert-cli

Recommended: Install with pipx for isolated environments:

pipx install msconvert-cli

Requirements: Docker must be installed and running.

Quick Start

# Convert with preset config
mscli /path/to/data/ -o ./output --sage

# Parallel processing (1 file per worker for Wine stability)
mscli /data/*.raw -o ./output --casanovo --workers 4

# With resource limits
mscli /data/*.raw -o ./output --sage --workers 4 --worker-cores 2.0 --worker-memory 4g

Presets

Pre-configured msconvert settings for common tools:

Use custom configs with -c my_config.txt or pass msconvert args directly.

Common Options

-o, --output-dir DIR      Output directory (required)
-w, --workers N          Number of parallel workers (default: 1)
-v, --verbose            Enable detailed logging
--log FILE               Custom log file path
-c, --config FILE        Custom msconvert config file

# Docker resource limits per worker
--worker-cores N         CPU cores (e.g., 2.0, 0.5)
--worker-memory SIZE     RAM limit (e.g., 4g, 2048m)
--worker-swap SIZE       Swap limit (set equal to memory to disable)
--worker-shm-size SIZE   Shared memory (default: 512m, increase for large files)

Examples

# Basic conversion
mscli file.raw -o ./output --sage

# Directory with parallel processing
mscli /data/raw_files/ -o ./output --blitzff --workers 4

# Custom config file
mscli file1.raw file2.raw -o ./output -c my_config.txt

# Verbose logging
mscli /data/*.raw -o ./output --casanovo -v

# Resource-limited workers
mscli /data/*.raw -o ./output --sage \
  --workers 4 \
  --worker-cores 2.0 \
  --worker-memory 4g \
  --worker-swap 4g

# Specific Docker image version
mscli data.raw -o ./output --sage \
  --docker-image proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.23310

Supported Formats

.raw, .wiff, .wiff2, .d, .baf, .fid, .yep, .tsf, .tdf, .mbi, .lcd, .ms, .cms1, .ms1, .cms2, .ms2, .t2d

Development

# Setup
git clone https://github.com/pgarrett-scripps/msconvert-cli.git
cd msconvert-cli
uv sync

# Quality checks
make check    # Run linters and type checking
make format   # Format code with ruff
make test     # Run tests

# Run locally
uv run mscli --help

License

Apache 2.0 - ProteoWizard license applies to the Docker image.

https://proteowizard.sourceforge.io/index.html

Citation

If using ProteoWizard, please cite: A cross-platform toolkit for mass spectrometry and proteomics. Chambers, M.C., MacLean, B., Burke, R., Amode, D., Ruderman, D.L., Neumann, S., Gatto, L., Fischer, B., Pratt, B., Egertson, J., Hoff, K., Kessner, D., Tasman, N., Shulman, N., Frewen, B., Baker, T.A., Brusniak, M.-Y., Paulse, C., Creasy, D., Flashner, L., Kani, K., Moulding, C., Seymour, S.L., Nuwaysir, L.M., Lefebvre, B., Kuhlmann, F., Roark, J., Rainer, P., Detlev, S., Hemenway, T., Huhmer, A., Langridge, J., Connolly, B., Chadick, T., Holly, K., Eckels, J., Deutsch, E.W., Moritz, R.L., Katz, J.E., Agus, D.B., MacCoss, M., Tabb, D.L. & Mallick, P. Nature Biotechnology 30, 918-920 (2012).