Merge pull request #1 from gavinmdouglas/nsti_float_fix

fixed NSTI option

Author: gavinmdouglas

q2_picrust2/_custom_tree_pipeline.py

@@ -11,10 +11,10 @@ def custom_tree_pipeline(table: biom.Table,
                          tree: skbio.TreeNode,
                          threads: int = 1,
                          hsp_method: str = "mp",
-                         max_nsti: int = 2)  -> (biom.Table,
-                                                 biom.Table,
-                                                 biom.Table,
-                                                 biom.Table):
+                         max_nsti: float = 2.0)  -> (biom.Table,
+                                                     biom.Table,
+                                                     biom.Table,
+                                                     biom.Table):
 
     # Run pipeline in temporary directory so that files are not saved locally.
     with TemporaryDirectory() as temp_dir:
@@ -52,12 +52,14 @@ def custom_tree_pipeline(table: biom.Table,
         EC_metagenome_out = path.join(picrust2_out, "EC_metagenome_out")
         system_call_check("metagenome_pipeline.py -i " + biom_infile + " -m " +
                           hsp_out_16S + ".tsv -f " + hsp_out_EC + ".tsv -p " +
-                          str(threads) + " -o " + EC_metagenome_out)
+                          str(threads) + " -o " + EC_metagenome_out +
+                          " --max_nsti " + str(max_nsti))
 
         KO_metagenome_out = path.join(picrust2_out, "KO_metagenome_out")
         system_call_check("metagenome_pipeline.py -i " + biom_infile + " -m " +
                           hsp_out_16S + ".tsv -f " + hsp_out_KO + ".tsv -p " +
-                          str(threads) + " -o " + KO_metagenome_out)
+                          str(threads) + " -o " + KO_metagenome_out +
+                          " --max_nsti " + str(max_nsti))
 
         # Run pathway inference step.
         pathways_out = path.join(picrust2_out, "pathways_out")

q2_picrust2/_full_pipeline.py

@@ -15,7 +15,7 @@ def full_pipeline(table: biom.Table,
                   seq : pd.Series,
                   threads: int = 1,
                   hsp_method: str = "mp",
-                  max_nsti: int = 2)  -> (biom.Table,
+                  max_nsti: float = 2.0)  -> (biom.Table,
                                                biom.Table,
                                                biom.Table,
                                                biom.Table):

q2_picrust2/plugin_setup.py

@@ -30,7 +30,7 @@
 
     parameters={'threads': Int % Range(1, None),
                 'hsp_method': Str % Choices(HSP_METHODS),
-                'max_nsti': Int % Range(0, None)},
+                'max_nsti': Float % Range(0.0, None)},
 
     outputs=[
        ('ko_metagenome', FeatureTable[Frequency]),
@@ -72,7 +72,7 @@
 
     parameters={'threads': Int % Range(1, None),
                 'hsp_method': Str % Choices(HSP_METHODS),
-                'max_nsti': Int % Range(0, None)},
+                'max_nsti': Float % Range(0.0, None)},
 
     outputs=[
        ('ko_metagenome', FeatureTable[Frequency]),