--- a/qiime2/qiime_diversity_beta-rarefaction.xml	Wed Jul 17 01:53:11 2019 -0400
+++ b/qiime2/qiime_diversity_beta-rarefaction.xml	Tue Aug 13 07:40:25 2019 -0400
@@ -8,15 +8,20 @@
 qiime diversity beta-rarefaction
 
 --i-table=$itable
+
 --p-metric=$pmetric
+
 --p-clustering-method=$pclusteringmethod
---p-sampling-depth="$psamplingdepth"
+
+#if str($psamplingdepth):
+ --p-sampling-depth="$psamplingdepth"
+#end if
 
 #if str($iphylogeny) != 'None':
  --i-phylogeny=$iphylogeny
 #end if
 
-#if $piterations:
+#if str($piterations):
  --p-iterations=$piterations
 #end if
 
@@ -28,20 +33,19 @@
  --p-color-scheme=$pcolorscheme
 #end if
 
+#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)
-
+#end if
 
 --o-visualization=ovisualization
 ;
-cp mmetadatafile.qza $mmetadatafile;
 qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
 && mv '$ovisualization.files_path/index.html' '$ovisualization';
@@ -109,7 +113,7 @@
 			<option value="RdYlGn_r">RdYlGn_r</option>
 		</param>
 
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
 			<param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata used for the Emperor jackknifed PCoA plot. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
 		</repeat>