--- a/qiime2/qiime_taxa_collapse.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_taxa_collapse.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,58 +1,45 @@
 <?xml version="1.0" ?>
-<tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.7">
-	<description> - Collapse features by their taxonomy at the specified level</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_taxa_collapse" name="qiime taxa collapse"
+      version="2020.8">
+  <description>Collapse features by their taxonomy at the specified level</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <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
 
-#if str($plevel):
- --p-level="$plevel"
+--i-taxonomy=$itaxonomy
+
+--p-level=$plevel
+
+--o-collapsed-table=ocollapsedtable
+
+#if str($examples) != 'None':
+--examples=$examples
 #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>
-		
+  ]]></command>
+  <inputs>
+    <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" type="text" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-		<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 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>
-		<data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Collapse features by their taxonomy at the specified level
-##########################################################
+###############################################################
 
 Collapse groups of features that have the same taxonomic assignment through
 the specified level. The frequencies of all features will be summed when
@@ -77,9 +64,9 @@
 collapsed_table : FeatureTable[Frequency]
     The resulting feature table, where all features are now taxonomic
     annotations with the user-specified number of levels.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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