--- a/amova.xml	Fri Jun 24 17:30:53 2016 -0400
+++ b/amova.xml	Thu May 18 18:27:46 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 "$dist" dist.dat &&
         ln -s "$design" design.dat &&
@@ -21,10 +24,11 @@
         )'
         | 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="design" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/>
+        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)"/>
         <param name="alpha" type="float" optional="true" min="0" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/>
         <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
         <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze." help="The set names are separated by dashes. The defualt is all sets in designfile">
@@ -58,7 +62,7 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations.
 
@@ -74,8 +78,8 @@
 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
 
 
-.. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
-.. _amova: http://www.mothur.org/wiki/Amova
+.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _amova: https://www.mothur.org/wiki/Amova
 
 ]]>
     </help>