--- a/collect.single.xml	Fri Jun 24 16:27:14 2016 -0400
+++ b/collect.single.xml	Thu May 18 18:29:07 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 "$otu" otu.dat &&
 
@@ -28,6 +31,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
         && rm otu.dat  ## don't want this collected into datacollection
     ]]></command>
     <inputs>
@@ -95,12 +99,12 @@
 @MOTHUR_OVERVIEW@
 
 
-**Command Documenation**
+**Command Documentation**
 
-The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _calculators: http://www.mothur.org/wiki/Calculators
-.. _collect.single: http://www.mothur.org/wiki/Collect.single
+.. _calculators: https://www.mothur.org/wiki/Calculators
+.. _collect.single: https://www.mothur.org/wiki/Collect.single
 ]]>
     </help>
     <expand macro="citations"/>