diff --git a/src/sourmash/cli/utils.py b/src/sourmash/cli/utils.py index 1725518747..2063fd09de 100644 --- a/src/sourmash/cli/utils.py +++ b/src/sourmash/cli/utils.py @@ -67,10 +67,14 @@ def range_limited_float_type(arg): return f -def add_tax_threshold_arg(parser, default=0.1): +def add_tax_threshold_arg(parser, containment_default=0.1, ani_default=None): parser.add_argument( - '--containment-threshold', default=default, type=range_limited_float_type, - help=f'minimum containment threshold for classification; default={default}' + '--containment-threshold', default=containment_default, type=range_limited_float_type, + help=f'minimum containment threshold for classification; default={containment_default}', + ) + parser.add_argument( + '--ani-threshold', '--aai-threshold', default=ani_default, type=range_limited_float_type, + help=f'minimum ANI threshold (nucleotide gather) or AAI threshold (protein gather) for classification; default={ani_default}', )