--- a/clearcut.xml	Fri Jun 24 16:39:06 2016 -0400
+++ b/clearcut.xml	Thu May 18 18:50:03 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 "$input.infile" input.infile.dat &&
 
@@ -34,6 +37,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -49,7 +53,7 @@
                 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
             </when>
             <when value="phylip">
-                <param name="infile" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
             </when>
         </conditional>
         <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
@@ -107,7 +111,7 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The clearcut_ command runs clearcut
 
@@ -118,7 +122,7 @@
 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input.  If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura).  Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
 
 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
-.. _clearcut: http://www.mothur.org/wiki/Clearcut
+.. _clearcut: https://www.mothur.org/wiki/Clearcut
 
 v.1.20.0: Trivial upgrade to Mothur 1.33
 ]]>