This CLI can be used to match the predicted metabolic products with experimental MS data.
matcher_cli <MS_DATA> <COMPOUNDS_TO_MATCH> <OUTPUT_DIRECTORY> [--tolerance=<FLOAT>] [--n_jobs=<INT>]| Argument | Example | Description | Default |
|---|---|---|---|
| ms_data <MS_DATA> | ms_data.tsv |
The path to the file containing the MS data. | |
| compounds_to_match <COMPOUNDS_TO_MATCH> | file.tsv |
The path to the file containing the predicted compounds to match with the MS data. | |
| output_directory <OUTPUT_DIRECTORY> | output/directory/ |
The path directory to save the results to. | |
| tolerance | 0.02 |
The mass tolerance to use when matching masses. | 0.02 |
| n_jobs | 6 |
The number of jobs to run in parallel (-1 uses all). | 1 |
More detailed information on these arguments and possible usages can be consulted in the main README.
matcher_cli ms_data.tsv compounds_to_match.tsv output_directory/ --tolerance=0.0015 --n_jobs=-1