From ca865a1e4edb89dff13c2b7d2544700e02f3118c Mon Sep 17 00:00:00 2001 From: Eric Marinier Date: Wed, 2 Aug 2023 14:01:28 -0500 Subject: [PATCH] Revert "Updating --mlst-scheme description." This reverts commit 62548d504b199987dd4563e6aeacf0b24956ded7. --- CHANGELOG.md | 1 - staramr/subcommand/Search.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3298a42..1f32ac0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,5 @@ # Unreleased -* Updated the help description of the --mlst-scheme parameter to include a more useful link for available schemas. * Switched to only officially supporting Python 3.7+ due to recent incompatibilities with Python 3.6 and some Python packages (numpy, biopython, and others). * Adds the ability to handle "complex" pbp5 mutations. When appriopriate many pbp5 point mutations will be reported as a single mutation. * Resfinder CGE-predicted phenotypes are now reported in the summary and detailed summary alongside existing predictions. diff --git a/staramr/subcommand/Search.py b/staramr/subcommand/Search.py index 2101830..490a48e 100644 --- a/staramr/subcommand/Search.py +++ b/staramr/subcommand/Search.py @@ -80,7 +80,7 @@ def _setup_args(self, arg_parser): arg_parser.add_argument('--ignore-invalid-files', action='store_true', dest='ignore_valid_files', help='Skips over invalid input files', required=False) arg_parser.add_argument('--mlst-scheme', action='store', dest='mlst_scheme', - help='Specify scheme name, visit https://github.com/tseemann/mlst/tree/master/db/pubmlst for supported scheme genera available. [None] ', required=False) + help='Specify scheme name, visit https://github.com/tseemann/mlst/blob/master/db/scheme_species_map.tab for supported scheme genus available. [None] ', required=False) arg_parser.add_argument('--genome-size-lower-bound', action='store', dest='genome_size_lower_bound', type=int, help='The lower bound for our genome size for the quality metrics. Defaults to 4 Mbp. [4000000].',