--- a/get.seqs.xml	Fri Jun 24 16:34:46 2016 -0400
+++ b/get.seqs.xml	Fri May 19 05:13:13 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 "$accnos" accnos.dat &&
         ln -s "$fasta_in" fasta_in.dat &&
@@ -51,6 +54,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
@@ -131,17 +135,17 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
 
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _list: http://www.mothur.org/wiki/List_file
-.. _align.report: http://www.mothur.org/wiki/Align.seqs
-.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
-.. _list.seqs: http://www.mothur.org/wiki/list.seqs
-.. _get.seqs: http://www.mothur.org/wiki/Get.seqs
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _align.report: https://www.mothur.org/wiki/Align.seqs
+.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
+.. _list.seqs: https://www.mothur.org/wiki/list.seqs
+.. _get.seqs: https://www.mothur.org/wiki/Get.seqs
 
 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
 ]]>