parser=argparse.ArgumentParser(description="Generates batch processing scripts for the MPI cluster to process tilt series subframes.")
# parser.add_argument("-f", "--file", help="create overlay for a single file",
parser.add_argument('-i','--input',nargs='?',default='.',help='Input MDOC file to process.')
parser.add_argument('-d','--outDir',nargs='?',default='.',help='Optional output directory to write scripts to.')
parser.add_argument('-dp','--dataPath',nargs='?',default='.',help='Optional override to use if the data is mounted in a different network base path.')
parser.add_argument('-cp','--clusterPath',nargs='?',default='/projects/project-nieverge/',help='Destination path of the HPC filesystem data directory.')
# parser.add_argument('-c', '--cutoff', nargs='?', type=float, default='1', help='The threshold of how many standard deviations above or below the a line must deviate before it is corrected')
# parser.add_argument('-g', '--graph', action='store_true', help='Store a graph of the corrected and uncorrected line intensities for debug purposes.')