diff --git a/src/bioontologies/cli.py b/src/bioontologies/cli.py index 6a8d89c..4a5627e 100644 --- a/src/bioontologies/cli.py +++ b/src/bioontologies/cli.py @@ -38,13 +38,17 @@ def main(): @main.command() @click.argument("prefix") @click.option("--directory", type=Path) -@click.option("--graph-id") -@click.option("--save-obograph", is_flag=True) +@click.option("--graph-id", help="The IRI of the graph to parse. Set this if it can't be guessed") +@click.option( + "--save-obograph", + is_flag=True, + help="Save intermediate OBO Graph JSON file if conversion from OWL is required", +) def index(prefix: str, graph_id: Optional[str], directory: Optional[Path], save_obograph: bool): """Generate a node index file.""" from .robot import get_obograph_by_prefix - prefix = bioregistry.normalize_prefix(prefix, strict=True) + prefix = bioregistry.normalize_prefix(prefix) if directory is None: directory = pystow.join("bioontologies", "index", prefix)