#This function handles the command line options.

parser = argparse.ArgumentParser();

parser.add_argument("-i", dest="input_file", help="A file containing a list of trees on which to run SDM and NJ OR a file containing a single tree on which to run r8s.");

parser.add_argument("-r", dest="r_output_file", help="A file name for R to write the Neighbor Joining tree.");

parser.add_argument("-j", dest="nj_opt", help="A boolean option to use SDM to create a consensus matrix and R to create a NJ tree. Default: 0.", type=int, default=0);

parser.add_argument("-o", dest="nj_outgroup", help="The outgroup by which the NJ tree will be rooted.");

parser.add_argument("-t", dest="reroot_opt", help="Boolean to reroot (1) the NJ tree or not (0). If set to 1, -o must also be specified. Default: 0", type=int, default=0);

parser.add_argument("-d", dest="div_est_opt", help="A boolean option to estimate divergence times from the NJ tree with r8s (1) or not (0). Default: 0.", type=int, default=0);

parser.add_argument("-e", dest="r8s_output_file", help="A file name for r8s to write the final output.");

parser.add_argument("-n", dest="num_sites", help="The total number of sites from the alignments used to make the tree; used by r8s.");

parser.add_argument("-s", dest="cal_specs", help="A list of PAIRS of species that define nodes you wish to constrain times on. Species within a pair should be separated by a comma, pairs should be separated by a space (eg 'pair1s1,pair1s2 pair2s1,pair2s2').");

parser.add_argument("-a", dest="cal_age", help="The calibration ages of the nodes defined by the species in -s. The order of this list corresponds to the order of -s. Separate ages by commas. If constraints are to be used the keywords min and/or max are used with hyphens (eg '324,min-99.9-max-121' defines one fixed age of 324 and one constrained age).");

parser.add_argument("-l", dest="log_opt", help="A boolean option to tell the script whether to create a logfile (1) or not (0). Default: 1", type=int, default=1);

parser.add_argument("-z", dest="script_logdir", help="A directory in which to place the script output directory. If none is specified, this will default to the directory of the input file");

parser.add_argument("-x", dest="logdir_suffix", help="A string to add on to the end of the output directory.");

args = parser.parse_args();

if errorflag == 0:

if args.input_file == None or args.nj_opt == None or args.nj_opt not in [0,1] or args.div_est_opt == None or args.div_est_opt not in [0,1]:

core.errorOut(1, "-i must always be defined. One of -j or -d must also always be defined as 1");

optParse(1);

if args.reroot_opt not in [0,1]:

core.errorOut(2, "-t must take values of either 1 or 0");

optParse(1);

if args.reroot_opt == 1 and args.nj_outgroup == None:

core.errorOut(3, "-When -t is set to 1, an outgroup must be specified with -o");

optParse(1);

if args.div_est_opt not in [0,1]:

core.errorOut(4, "-d must take values of either 1 or 0");

optParse(1);

elif args.div_est_opt == 1:

if args.r8s_output_file == None or args.num_sites == None or args.cal_specs == None or args.cal_age == None:

core.errorOut(5, "You are missing one or more of the options for div time estimation with r8s. -e, -n, -s, and -a must all be defined");

optParse(1);

else:

if args.cal_specs.find(" ") != -1 and args.cal_age.find(",") != -1:

cal_specs = args.cal_specs.split(" ");

cal_age = args.cal_age.split(",");

else:

cal_specs = [args.cal_specs];

cal_age = [args.cal_age];

if len(cal_specs) != len(cal_age):

core.errorOut(6, "You must enter the same number of calibration nodes (-s) and calibration ages (-a)");

optParse(1);

else:

args.r8s_output_file = None;

args.num_sites = None;

cal_specs = None;

cal_age = None;

if args.log_opt not in [0,1]:

core.errorOut(7, "-l must take values of either 1 or 0");

optParse(1);

return args.input_file, args.r_output_file, args.nj_opt, args.nj_outgroup, args.reroot_opt, args.div_est_opt, args.r8s_output_file, args.num_sites, cal_specs, cal_age, args.log_opt, args.script_logdir, args.logdir_suffix;

elif errorflag == 1:

parser.print_help();