tofspec CLI Documentation#
tofspec#
tofspec [OPTIONS] COMMAND [ARGS]...
Options
- --version#
Show the version and exit.
concat#
Concatenate FILES together and save to OUTPUT. FILES is the collection or list of files that you are concatenating together. They can be provided as a list or by using a wildcard and providing the path with wildcard.
tofspec concat [OPTIONS] [FILES]...
Options
- -o, --output <output>#
The filepath where you would like to save the file
Arguments
- FILES#
Optional argument(s)
config#
Use FILE to construct a peak list configuration .yaml file that will be used to integrate peaks and label / group data.
tofspec config [OPTIONS] FILE
Options
- -s, --smiles#
Does FILE have a smiles column?
- -ion, --ion#
Does FILE have an ion column instead of a mf column?
- -n, --name <name>#
Name for the peak list
- -a, --author <author>#
Author of the peak list
- -o, --output <output>#
The filepath where you would like to save the peak list
Arguments
- FILE#
Required argument
integrate-peaks#
Convert FILE, a matrix of raw PTR-TOF-MS data (TOF bins X timestamps) to a time series of integrated ion counts/concentrations for ions specified in the peak list (CONFIG).
tofspec integrate-peaks [OPTIONS] FILE
Options
- -c, --config <config>#
The peak list .yml file that guides the integration process
- -ts, --tscol <tscol>#
Column in FILE which contains timestamps
- -i, --ignore <ignore>#
Names of metadata column(s) which should be ignored in the integration and passed to OUTPUT untouched
- -col, --columns <columns>#
Choose either molecular formula (mf) or SMILES string (smiles) as the column names of OUTPUT
- Options
smiles | mf
- -o, --output <output>#
The filepath where you would like to save the file
Arguments
- FILE#
Required argument
label#
Convert FILE, a matrix of compound counts/concentrations, to a time series of integrated substructure/functional group concentrations. For more info on how to choose different substructures…
tofspec label [OPTIONS] FILE
Options
- -ts, --tscol <tscol>#
column in FILE which contains timestamps
- -i, --ignore <ignore>#
names of metadata column(s) which should not be included in the integration but should be passed to OUTPUT
- -col, --columns <columns>#
choose either molecular formula (mf) or SMILES string (smiles) as the column names of FILE
- Options
smiles | mf
- -o, --output <output>#
The filepath where you would like to save the file
Arguments
- FILE#
Required argument
load#
Parse mass spec FILE and save relevant data to OUTPUT. Read TOF data matrix from FILE. The structure of FILE is determined by the optional –instrument and –format arguments. Currently, only ‘vocus’ and ‘h5’ are accepted.
tofspec load [OPTIONS] FILE
Options
- -i, --instrument <instrument>#
The instrument that FILE comes from
- -f, --format <format>#
The format/file extension of FILE
- -m, --metadata#
Does the file include metadata?
- -o, --output <output>#
The filepath where you would like to save the file
Arguments
- FILE#
Required argument
merge#
Merge FILES together and save to OUTPUT.
tofspec merge [OPTIONS] [FILES]...
Options
- -ts, --tscol <tscol>#
The column by which to join the files
- -o, --output <output>#
The filepath where you would like to save the file
- -v, --verbose#
Enable verbose mode (debugging)
Arguments
- FILES#
Optional argument(s)