--- a/sort.seqs.xml	Fri Jun 24 16:50:30 2016 -0400
+++ b/sort.seqs.xml	Thu May 18 18:10:17 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 "$fasta_in" fasta_in.dat &&
         ln -s "$qfile_in" qfile_in.dat &&
@@ -45,6 +48,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
@@ -115,12 +119,12 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
 
-.. _sort.seqs: http://www.mothur.org/wiki/Sort.seqs
+.. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
 
 ]]>
     </help>