run.py

#!/usr/bin/env python3
import argparse
parser = argparse.ArgumentParser(description='BIDS App entrypoint script '
                    'to extract time-series from resting-state.')
parser.add_argument('bids_dir', help='The directory with the input dataset '
                    'formatted according to the BIDS standard.')
parser.add_argument('output_dir', help='The directory where the output files '
                    'should be stored. If you are running group level analysis '
                    'this folder should be prepopulated with the results of the'
                    'participant level analysis.')
parser.add_argument('analysis_level', help='Level of the analysis that will be performed. '
                    'Multiple participant level analyses can be run independently '
                    '(in parallel) using the same output_dir.',
                    choices=['participant', 'group'])
parser.add_argument('--participant_label', help='The label(s) of the participant(s) that should be analyzed. The label '
                   'corresponds to sub-<participant_label> from the BIDS spec '
                   '(so it does not include "sub-"). If this parameter is not '
                   'provided all subjects should be analyzed. Multiple '
                   'participants can be specified with a space separated list.',
                   nargs="+")

args = parser.parse_args()

from main import main
main(args)