--- a/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Mon Aug 05 01:29:30 2019 -0400
+++ b/qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml	Tue Aug 13 07:46:48 2019 -0400
@@ -5,29 +5,34 @@
 		<requirement type="package" version="2019.4">qiime2</requirement>
 	</requirements>
 	<command><![CDATA[
-qiime feature-classifier fit-classifier-naive-bayes
-
---i-reference-reads=$ireferencereads
 
 
 #if str( $id_to_taxonomy_fp.selector ) == 'history'
 	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
-	--i-reference-taxonomy '$tax'
 #else:
-	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
-	--i-reference-taxonomy '$tax'
+	#set $tax_path = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+	qiime tools import --type 'FeatureData[Taxonomy]'  --source-format HeaderlessTSVTaxonomyFormat --input-path $tax_path --output-path ref-taxonomy.qza;
+	#set $tax='ref-taxonomy.qza'
 #end if
 
 
+qiime feature-classifier fit-classifier-naive-bayes
+
+
+--i-reference-taxonomy '$tax'
+
+
+--i-reference-reads=$ireferencereads
+
 #if str($iclassweight) != 'None':
  --i-class-weight=$iclassweight
 #end if
 
-#if $pclassifyalpha:
+#if str($pclassifyalpha):
  --p-classify--alpha=$pclassifyalpha
 #end if
 
-#if $pclassifychunksize:
+#if str($pclassifychunksize):
  --p-classify--chunk-size=$pclassifychunksize
 #end if
 
@@ -119,7 +124,7 @@
  --p-no-feat-ext--lowercase
 #end if
 
-#if $pfeatextnfeatures:
+#if str($pfeatextnfeatures):
  --p-feat-ext--n-features=$pfeatextnfeatures
 #end if