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")