--- a/qiime2/qiime_diversity_adonis.xml	Wed Jul 17 01:53:11 2019 -0400
+++ b/qiime2/qiime_diversity_adonis.xml	Tue Aug 13 07:40:25 2019 -0400
@@ -10,22 +10,29 @@
 --i-distance-matrix=$idistancematrix
 
 
+#if $input_files_mmetadatafile:
 #def list_dict_to_string(list_dict):
   #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
   #for d in list_dict[1:]:
-	  #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+	  #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
   #end for
   #return $file_list
 #end def
-
---m-metadata-file=$list_dict_to_string("$input_files_mmetadatafile")
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+#end if
 
 
 
+#if '__sq__' in str($pformula):
+  #set $pformula_temp = $pformula.replace('__sq__', "'")
+  #set $pformula = $pformula_temp
+#end if
 
 --p-formula="$pformula"
 
-#if $ppermutations:
+
+
+#if str($ppermutations):
  --p-permutations=$ppermutations
 #end if
 
@@ -45,7 +52,7 @@
 		<param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text"/>
 		<param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
 			<param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
 		</repeat>
 	</inputs>