--- a/remove.dists.xml	Fri Jun 24 16:46:24 2016 -0400
+++ b/remove.dists.xml	Thu May 18 18:18:47 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 "$accnos" accnos.dat &&
         ln -s "$input.dist" input_dist.dat &&
@@ -20,6 +23,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -31,7 +35,7 @@
                 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
             </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"/>
             </when>
         </conditional>
         <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
@@ -54,11 +58,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.
 
-.. _remove.dists: http://www.mothur.org/wiki/Remove.dists
+.. _remove.dists: https://www.mothur.org/wiki/Remove.dists
 
 ]]>
     </help>