CLI docs

gseapy/__main__.py

@@ -228,6 +228,8 @@ def add_singlesample_parser(subparsers):
                            default='rank', metavar='normalize',
                            choices=("rank", "log", "log_rank", "custom"),
                            help="Sample normalization method. Choose from {'rank', 'log', 'log_rank','custom'}. Default: rank")
+    group_opt.add_argument("--no-scale", action='store_false', dest='scale', default=True,
+                           help="If the flag was set, don't normalize the enrichment scores by number of genes.")
     group_opt.add_argument("-n", "--permu-num", dest = "n", action="store", type=int, default=1000, metavar='perNum',
                            help="Number of random permutations. For calculating esnulls. Default: 1000")
     group_opt.add_argument("--min-size", dest="mins", action="store", type=int, default=15, metavar='int',
@@ -236,8 +238,6 @@ def add_singlesample_parser(subparsers):
                            help="Max size of input genes presented in Gene Sets. Default: 2000")
     group_opt.add_argument("-w", "--weight", action='store', dest='weight', default=0.25, type=float, metavar='weight',
                            help='Weighted_score of rank_metrics.For weighting input genes.default: 0.25',)
-    group_opt.add_argument("--no-scale", action='store_false', dest='scale', default=True,
-                           help="If the flag was set, don't normalize the enrichment scores by number of genes in the gene sets.")
     group_opt.add_argument("-a", "--ascending", action='store_true', dest='ascending', default=False,
                            help='Rank metric sorting order. If the -a flag was chosen, then ascending equals to True. Default: False.')
     group_opt.add_argument("--graph", dest = "graph", action="store", type=int, default=20, metavar='int',