--- a/get.lineage.xml	Fri Jun 24 16:32:26 2016 -0400
+++ b/get.lineage.xml	Fri May 19 04:25:37 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@
+
         #import re
         ## create symlinks to input datasets
         ln -s "$file.taxonomy" file.taxonomy.dat &&
@@ -60,6 +63,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="file">
@@ -186,16 +190,16 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The get.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.
 
-.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
-.. _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
-.. _get.lineage: http://www.mothur.org/wiki/Get.lineage
+.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
+.. _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
+.. _get.lineage: https://www.mothur.org/wiki/Get.lineage
 
 ]]>
     </help>