added cureated_indet as parameter

q2_amr/amrfinderplus/sample_data.py

@@ -22,6 +22,7 @@ def annotate_sample_data_amrfinderplus(
     plus: bool = False,
     report_all_equal: bool = False,
     ident_min: float = None,
+    curated_ident: bool = False,
     coverage_min: float = 0.5,
     translation_table: str = "11",
     threads: int = None,

q2_amr/amrfinderplus/tests/test_utils.py

@@ -20,6 +20,7 @@ def test_run_amrfinderplus_n(self, mock_run_command):
             plus=True,
             report_all_equal=True,
             ident_min=1,
+            curated_ident=False,
             coverage_min=1,
             translation_table="11",
             threads=4,
@@ -73,6 +74,7 @@ def test_run_amrfinderplus_n_minimal(self, mock_run_command):
             plus=False,
             report_all_equal=False,
             ident_min=None,
+            curated_ident=True,
             coverage_min=None,
             translation_table=None,
             threads=None,
@@ -85,6 +87,8 @@ def test_run_amrfinderplus_n_minimal(self, mock_run_command):
                 "-o",
                 "path_dir/amr_annotations.tsv",
                 "--print_node",
+                "--ident_min",
+                "-1",
             ],
             "path_dir",
             verbose=True,

q2_amr/amrfinderplus/utils.py

@@ -13,6 +13,7 @@ def run_amrfinderplus_n(
     plus,
     report_all_equal,
     ident_min,
+    curated_ident,
     coverage_min,
     translation_table,
     threads,
@@ -60,8 +61,10 @@ def run_amrfinderplus_n(
         cmd.append("--plus")
     if report_all_equal:
         cmd.append("--report_all_equal")
-    if ident_min:
+    if ident_min and not curated_ident:
         cmd.extend(["--ident_min", str(ident_min)])
+    if curated_ident:
+        cmd.extend(["--ident_min", "-1"])
     if coverage_min:
         cmd.extend(["--coverage_min", str(coverage_min)])
     if translation_table:

q2_amr/plugin_setup.py

@@ -1153,7 +1153,8 @@
         "organism": Str % Choices(organisms),
         "plus": Bool,
         "report_all_equal": Bool,
-        "ident_min": Float % Range(-1, 1, inclusive_start=True, inclusive_end=True),
+        "ident_min": Float % Range(0, 1, inclusive_start=True, inclusive_end=True),
+        "curated_ident": Bool,
         "coverage_min": Float % Range(0, 1, inclusive_start=True, inclusive_end=True),
         "translation_table": Str % Choices(translation_tables),
         "threads": Int % Range(0, None, inclusive_start=False),
@@ -1180,11 +1181,13 @@
         "and Name of closest sequence will be different showing "
         "each of the database proteins that are equally close to "
         "the query sequence.",
-        "ident_min": "Minimum identity for a blast-based hit hit (Methods BLAST or "
-        "PARTIAL). -1 means use the curated threshold if it exists and "
-        "0.9 otherwise. Setting this value to something other than -1 "
+        "ident_min": "Minimum identity for a blast-based hit (Methods BLAST or "
+        "PARTIAL). Setting this value to something other than -1 "
         "will override curated similarity cutoffs. We only recommend "
         "using this option if you have a specific reason.",
+        "curated_ident": "Use the curated threshold for a blast-based hit, if it "
+        "exists and 0.9 otherwise. This will overwrite the value specified with the "
+        "'ident_min' parameter",
         "coverage_min": "Minimum proportion of reference gene covered for a "
         "BLAST-based hit (Methods BLAST or PARTIAL).",
         "translation_table": "Translation table used for BLASTX.",