--- a/qiime2/qiime_taxa_collapse.xml	Mon Aug 05 01:29:30 2019 -0400
+++ b/qiime2/qiime_taxa_collapse.xml	Tue Aug 13 07:46:48 2019 -0400
@@ -7,17 +7,44 @@
 	<command><![CDATA[
 qiime taxa collapse
 
+#if str( $id_to_taxonomy_fp.selector ) == 'history'
+	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
+	--i-taxonomy '$tax'
+#else:
+	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
+	--i-taxonomy '$tax'
+#end if
+
+
 --i-table=$itable
---i-taxonomy=$itaxonomy
---p-level="$plevel"
+
+#if str($plevel):
+ --p-level="$plevel"
+#end if
 
 --o-collapsed-table=ocollapsedtable
 ;
 cp ocollapsedtable.qza $ocollapsedtable
 	]]></command>
 	<inputs>
+
+		<conditional name="id_to_taxonomy_fp" optional="True">
+		   <param name="selector" type="select" label="Reference taxonomy to query">
+			  <option value="cached">Public databases</option>
+			  <option value="history">Databases from your history</option>
+		   </param>
+		   <when value="cached">
+			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
+				 <options from_data_table="qiime_taxonomy" />
+			  </param>
+		   </when>
+		   <when value="history">
+			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
+		   </when>
+		</conditional>
+		
+
 		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed.             [required]" name="itable" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data"/>
 		<param label="--p-level: INTEGER      The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation.       [required]" name="plevel" optional="False" value="" type="integer"/>
 	</inputs>
 	<outputs>