--- a/hcluster.xml	Fri Jun 24 16:35:04 2016 -0400
+++ b/hcluster.xml	Thu May 18 18:46:34 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$matrix.dist" matrix.dist.dat &&
         ln -s "$matrix.name" matrix.name.dat &&
@@ -31,6 +34,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="matrix">
@@ -43,7 +47,7 @@
                 <param name="name" type="data" format="mothur.names" label="name - Names"/>
             </when>
             <when value="phylip">
-                <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
                 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
             </when>
         </conditional>
@@ -76,8 +80,16 @@
         <test><!-- test with phylip input-->
             <param name="format" value="phylip"/>
             <param name="dist" value="98_sq_phylip_amazon.dist"/>
-            <output name="rabund" md5="aafe1357a2f76e2d05e52c5a26838061" ftype="mothur.rabund"/>
-            <output name="sabund" md5="103af393a98579aec05e3cc935343a3c" ftype="mothur.sabund"/>
+            <output name="rabund" ftype="mothur.rabund">
+                <assert_contents>
+                    <has_line_matching expression="0\.[0-9]+(\t[0-9]+)+"/>
+                </assert_contents>
+            </output>
+            <output name="sabund" ftype="mothur.sabund">
+                <assert_contents>
+                    <has_line_matching expression="0\.[0-9]+(\t[0-9]+)+"/>
+                </assert_contents>
+            </output>
             <output name="otulist" ftype="mothur.list">
                 <assert_contents>
                     <has_text text="unique"/>
@@ -110,17 +122,16 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The hcluster_ command assign sequences to OTUs (Operational Taxonomy Unit).  The assignment is based on a phylip-formatted_distance_matrix_ or a  column-formatted_distance_matrix_ and name_ file.  It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
 
-.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
-.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _list: http://www.mothur.org/wiki/List_file
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _sabund: http://www.mothur.org/wiki/Sabund_file
-.. _hcluster: http://www.mothur.org/wiki/Hcluster
+.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _sabund: https://www.mothur.org/wiki/Sabund_file
 
 ]]>
     </help>