def _add_arguments(self, parser):
Command._add_arguments(self, parser)
parser.add_argument("data_path", metavar="DATA",
help="File containing the data matrix in TDM format")
parser.add_argument("-N", "--samplings", dest="num_samplings", type=int, default=10000, metavar="NUMBER",
help="Number of samplings to compute the FM bias pvalue")
parser.add_argument("-e", "--estimator", dest="estimator", metavar="ESTIMATOR",
choices=["mean", "median"], default="mean",
help="Test estimator for computation.")
parser.add_argument("--gt", "--gene-threshold", dest="mut_gene_threshold", type=int, default=2, metavar="THRESHOLD",
help="Minimum number of mutations per gene to compute the FM bias")
parser.add_argument("--pt", "--pathway-threshold", dest="mut_pathway_threshold", type=int, default=10, metavar="THRESHOLD",
help="Minimum number of mutations per pathway to compute the FM bias")
parser.add_argument("-s", "--slices", dest="slices", metavar="SLICES",
help="Slices to process separated by commas")
parser.add_argument("-m", "--mapping", dest="mapping", metavar="PATH",
help="File with mappings between genes and pathways to be analysed")
parser.add_argument("-f", "--filter", dest="filter", metavar="PATH",
help="File containing the features to be filtered. By default labels are includes,"
" labels preceded with - are excludes.")
parser.add_argument("--save-data", dest="save_data", default=False, action="store_true",
help="The input data matrix will be saved")
parser.add_argument("--save-analysis", dest="save_analysis", default=False, action="store_true",
help="The analysis results will be saved")
def _add_arguments(self, parser):
Command._add_arguments(self, parser)
parser.add_argument("data_paths", metavar="DATA", nargs="+",
help="Files with the results to be combined")
parser.add_argument("-m", dest="method", metavar="NAME",
choices=method_names(),
help="The NAME of the method to combine values")
parser.add_argument("--save-data", dest="save_data", default=False, action="store_true",
help="The input data matrix will be saved")
