diff --git a/augur/filter/__init__.py b/augur/filter/__init__.py index ac8ad88ff..947875258 100644 --- a/augur/filter/__init__.py +++ b/augur/filter/__init__.py @@ -67,9 +67,9 @@ def register_arguments(parser): subsample_limits_group = subsample_group.add_mutually_exclusive_group() subsample_limits_group.add_argument('--sequences-per-group', type=int, help="subsample to no more than this number of sequences per category") subsample_limits_group.add_argument('--subsample-max-sequences', type=int, help="subsample to no more than this number of sequences; can be used without the group_by argument") - probabilistic_sampling_group = subsample_group.add_mutually_exclusive_group() - probabilistic_sampling_group.add_argument('--probabilistic-sampling', action='store_true', help="Allow probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided.") - probabilistic_sampling_group.add_argument('--no-probabilistic-sampling', action='store_false', dest='probabilistic_sampling') + group_size_options = subsample_group.add_mutually_exclusive_group() + group_size_options.add_argument('--probabilistic-sampling', action='store_true', help="Allow probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided.") + group_size_options.add_argument('--no-probabilistic-sampling', action='store_false', dest='probabilistic_sampling') subsample_group.add_argument('--priority', type=str, help="""tab-delimited file with list of priority scores for strains (e.g., "\\t") and no header. When scores are provided, Augur converts scores to floating point values, sorts strains within each subsampling group from highest to lowest priority, and selects the top N strains per group where N is the calculated or requested number of strains per group. Higher numbers indicate higher priority.