Limit maxiterate and retree params to range

Author: fethalen

q2_alignment/_mafft.py

@@ -110,14 +110,10 @@ def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments,
     if strategy:
         cmd += [("--" + strategy)]
 
-    # --maxiterate is set to 0 by default, so we only pass this argument onto
-    # MAFFT if it deviates from this value.
-    if maxiterate not in (None, 0):
+    if maxiterate is not None:
         cmd += ['--maxiterate', str(maxiterate)]
 
-    # --retree is set to 2 by default, so we only pass this argument onto
-    # MAFFT if it deviates from this value.
-    if retree not in (None, 2):
+    if retree is not None:
         cmd += ['--retree', str(retree)]
 
     if alignment_fp is not None:

q2_alignment/plugin_setup.py

@@ -19,8 +19,8 @@
     "strategy": Str % Choices({
         "auto", "nofft", "globalpair", "localpair", "genafpair",
     }),
-    "maxiterate": Int,
-    "retree": Int,
+    "maxiterate": Int % Range(0, None),
+    "retree": Int % Range(0, None),
 }
 mafft_param_descriptions = {
     "n_threads": "The number of threads. (Use `auto` to automatically use "