def handle_program_options():
    """Parses the given options passed in at the command line."""
    parser = argparse.ArgumentParser(description="Calculate the alpha diversity\
                                     of a set of samples using one or more \
                                     metrics and output a kernal density \
                                     estimator-smoothed histogram of the \
                                     results.")
    parser.add_argument("-m", "--map_file",
                        help="QIIME mapping file.")
    parser.add_argument("-i", "--biom_fp",
                        help="Path to the BIOM table")
    parser.add_argument("-c", "--category",
                        help="Specific category from the mapping file.")
    parser.add_argument("-d", "--diversity", default=["shannon"], nargs="+",
                        help="The alpha diversity metric. Default \
                             value is 'shannon', which will calculate the Shannon\
                             entropy. Multiple metrics can be specified (space separated).\
                             The full list of metrics is available at:\
                             http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.\
                             Beta diversity metrics will be supported in the future.")
    parser.add_argument("--x_label", default=[None], nargs="+",
                        help="The name of the diversity metric to be displayed on the\
                        plot as the X-axis label. If multiple metrics are specified,\
                        then multiple entries for the X-axis label should be given.")
    parser.add_argument("--color_by",
                        help="A column name in the mapping file containing\
                              hexadecimal (#FF0000) color values that will\
                              be used to color the groups. Each sample ID must\
                              have a color entry.")
    parser.add_argument("--plot_title", default="",
                        help="A descriptive title that will appear at the top \
                        of the output plot. Surround with quotes if there are\
                        spaces in the title.")
    parser.add_argument("-o", "--output_dir", default=".",
                        help="The directory plots will be saved to.")
    parser.add_argument("--image_type", default="png",
                        help="The type of image to save: png, svg, pdf, eps, etc...")
    parser.add_argument("--save_calculations",
                        help="Path and name of text file to store the calculated "
                        "diversity metrics.")
    parser.add_argument("--suppress_stats", action="store_true", help="Do not display "
                        "significance testing results which are shown by default.")
    parser.add_argument("--show_available_metrics", action="store_true",
                        help="Supply this parameter to see which alpha diversity metrics "
                             " are available for usage. No calculations will be performed"
                             " if this parameter is provided.")
    return parser.parse_args()
Parses the given options passed in at the command line.