--- a/count.seqs.xml	Fri Jun 24 16:28:37 2016 -0400
+++ b/count.seqs.xml	Thu May 18 18:16:37 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@
+
         ## create symlinks to input datasets
         ln -s "$name" name.dat &&
         #if $grouping.use == "yes":
@@ -17,13 +20,14 @@
             #if $grouping.use == "yes":
                 group=grouping.group.dat,
                 #if $grouping.groups:
-                    groups=$grouping.groups,
+                    groups=${ str($grouping.groups).replace(",","-") },
                 #end if
             #end if
             large=$large
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
@@ -70,20 +74,28 @@
             <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
             <expand macro="logfile-test"/>
         </test>
+        <test> <!-- test with group file and multiple groups -->
+            <param name="name" value="amazon.names"/>
+            <param name="use" value="yes"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="pasture,forest"/>
+            <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
+            <expand macro="logfile-test"/>
+        </test>
     </tests>
     <help>
 <![CDATA[
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown.
 
-.. _name: http://www.mothur.org/wiki/Name_file
-.. _group: http://www.mothur.org/wiki/Group_file
-.. _count.seqs: http://www.mothur.org/wiki/Count.seqs
-.. _count_table: http://www.mothur.org/wiki/Count_File
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _count.seqs: https://www.mothur.org/wiki/Count.seqs
+.. _count_table: https://www.mothur.org/wiki/Count_File
 
 v.1.21.0: Updated to Mothur 1.33
 ]]>