Command Line Interface

$ amimspy --help

Executing amimspy version 0.1.0
usage: __main__.py [-h]
                   {process-scans,process-samples,hdf5-pm-to-txt,hdf5-pls-to-txt}
                   ...

Python package for processing acoustic mist ionisation-mass spectrometry
-based metabolomics and lipidomics data

positional arguments:
  {process-scans,process-samples,hdf5-pm-to-txt,hdf5-pls-to-txt}
    process-scans       Process and align scans within samples.
    process-samples     Process and align samples.
    hdf5-pm-to-txt      Write HDF5 output (peak matrix) to text format.
    hdf5-pls-to-txt     Write HDF5 output (peak lists) to text format.

optional arguments:
  -h, --help            show this help message and exit

$ amimspy process-scans --help

Executing amimspy version 0.1.0
usage: __main__.py process-scans [-h] -i source [source ...] -ms source
                             [source ...] -o OUTPUT -f FAILED_WELLS -pr
                             PROCESSED_SCANS
                             [-m {all_scans,on_scans,off_scans,on_scan_no_edge}]
                             [-d ID_SNR] [-t ID_TOL] [-s SNR_THRESHOLD]
                             [-n MIN_SCANS] [-r RSD_THRESHOLD]
                             [-fr MIN_FRACTION] -p PPM [-l METALIST]

optional arguments:
  -h, --help            show this help message and exit
  -i source [source ...], --input source [source ...]
                        Absolute or relative path to the *.mzml file(s). Must
                        be in same order as 'metascans *txt files'
  -ms source [source ...], --metascans source [source ...]
                        Absolute or relative path to the comma-delimited *.txt
                        metadata file. Must be in same order and 'input' *mzml
                        files. Header names must contain and be in the
                        following order names =['barcode', 'date/time', 'row',
                        'col', 'scan', 'ejection time', 'NA'] as output by MS-
                        Parser tool
  -o OUTPUT, --output OUTPUT
                        Absolute or relative path to the output file
  -f FAILED_WELLS, --failed-wells FAILED_WELLS
                        Absolute or relative path to the *.txt output of which
                        well failed
  -pr PROCESSED_SCANS, --processed_scans PROCESSED_SCANS
                        Absolute or relative path to the *.txt output of which
                        well failed
  -m {all_scans,on_scans,off_scans,on_scan_no_edge}, --method {all_scans,on_scans,off_scans,on_scan_no_edge}
                        Method to define which scans to extract data from.
                        DEFAULT = on_scans_no_edge
  -d ID_SNR, --id-snr ID_SNR
                        For identifying on/off scans: Hard SNR threshold for
                        differentiating between on/off scans. DEFAULT = 15
  -t ID_TOL, --id-tol ID_TOL
                        For identifying on/off scans: Number of features with
                        SNR > threshold to tolerate in off scans. DEFAULT = 3
  -s SNR_THRESHOLD, --snr-threshold SNR_THRESHOLD
                        SNR threshold to remove noise features. DEFAULT = 2
  -n MIN_SCANS, --min-scans MIN_SCANS
                        Minimum number of scans required to be labelled on
                        within a well for sample to be taken forward. DEFAULT
                        = 0
  -r RSD_THRESHOLD, --rsd-threshold RSD_THRESHOLD
                        RSD filter (scan level): Threshold of RSD of features
                        across scans in sample for it to be retained. DEFAULT
                        = None
  -fr MIN_FRACTION, --min-fraction MIN_FRACTION
                        Minimum fraction a peak has to be present. Use 0.0 to
                        not apply this filter.
  -p PPM, --ppm PPM     Aligning scans: m/z precision (ppm) to align scans in
                        sample - REQUIRED PARAMETER!
  -l METALIST, --metalist METALIST
                        Absolute or relative path to the tab-delimited *.txt
                        file that include the name of the data files (*.mzml)
                        and meta data. Column names: filename, replicate,
                        batch, injectionOrder, classLabel.