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MSDataMatcher CLI

This CLI can be used to match the predicted metabolic products with experimental MS data.

Command Line Interface

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.

Example:

matcher_cli ms_data.tsv compounds_to_match.tsv output_directory/ --tolerance=0.0015 --n_jobs=-1