--- a/make.shared.xml	Fri Jun 24 16:38:49 2016 -0400
+++ b/make.shared.xml	Fri May 19 04:28:22 2017 -0400
@@ -1,11 +1,14 @@
-<tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0" force_history_refresh="True">
+<tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0">
     <description>Make a shared file from a list and a group</description>
     <macros>
         <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 "$intype.otu" intype_otu.dat &&
         #if $intype.infile == "otulist":
@@ -31,7 +34,8 @@
             #end if
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur &&
+        | mothur
+        | tee mothur.out.log &&
 
         ## move output files to correct destination
         mv mothur.*.logfile "$logfile" &&
@@ -68,11 +72,11 @@
         <expand macro="logfile-output"/>
         <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
         <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
-            <filter>groups</filter>
+            <filter>intype['group'].ext == "mothur.groups"</filter>
         </data>
         <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label">
             <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
-            <filter>groups</filter>
+            <filter>intype['groups']</filter>
         </collection>
     </outputs>
     <tests>
@@ -107,16 +111,16 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.
 
 
-.. _list: http://www.mothur.org/wiki/List_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _rabund: http://www.mothur.org/wiki/Rabund_file
-.. _make.shared: http://www.mothur.org/wiki/Make.shared
+.. _list: https://www.mothur.org/wiki/List_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _rabund: https://www.mothur.org/wiki/Rabund_file
+.. _make.shared: https://www.mothur.org/wiki/Make.shared
 ]]>
     </help>
     <expand macro="citations"/>