--- a/nmds.xml	Fri Jun 24 16:42:28 2016 -0400
+++ b/nmds.xml	Thu May 18 18:41:40 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 "$dist" dist.dat &&
         ln -s "$axes" axes.dat &&
@@ -28,9 +31,10 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
-        <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="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
         <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
         <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
@@ -64,14 +68,14 @@
 
 @MOTHUR_OVERVIEW@
 
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
+.. _Mothur: https://www.mothur.org/wiki/Main_Page
 
-**Command Documenation**
+**Command Documentation**
 
 The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.
 
-.. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
-.. _nmds: http://www.mothur.org/wiki/Nmds
+.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _nmds: https://www.mothur.org/wiki/Nmds
 
 v1.20.0: Updated to mothur 1.33
 ]]>