--- a/count.groups.xml	Tue Sep 05 16:43:14 2017 -0400
+++ b/count.groups.xml	Wed Feb 14 09:50:47 2018 -0500
@@ -7,41 +7,41 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$group" group.dat &&
-        #if $groupnames.source == "accnos":
-            ln -s "$groupnames.accnos" groupnames.accnos.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$group' group.dat &&
+#if $groupnames.source == "accnos":
+    ln -s '$groupnames.accnos' groupnames.accnos.dat &&
+#end if
 
-        echo 'count.groups(
-            #if $group.is_of_type("mothur.shared"):
-                shared=group.dat
-            #elif $group.is_of_type("mothur.count_table"):
-                count=group.dat
-            #else:
-                group=group.dat
-            #end if
-            #if $groupnames.source == "groups":
-                #if $groupnames.groups:
-                    ,groups=$groupnames.groups
-                #end if
-            #elif $groupnames.source == "accnos":
-                #if $groupnames.accnos:
-                    ,accnos=groupnames.accnos.dat
-                #end if
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log &&
+echo 'count.groups(
+    #if $group.is_of_type("mothur.shared"):
+        shared=group.dat
+    #elif $group.is_of_type("mothur.count_table"):
+        count=group.dat
+    #else:
+        group=group.dat
+    #end if
+    #if $groupnames.source == "groups":
+        #if $groupnames.groups:
+            ,groups=${ str($groupnames.groups).replace(",","-") }
+        #end if
+    #elif $groupnames.source == "accnos":
+        #if $groupnames.accnos:
+            ,accnos=groupnames.accnos.dat
+        #end if
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log &&
 
-        ## parse relevant tool output from logfile to file
-        cat mothur.*.logfile
-        | head -n-7
-        | sed '1,29d'
-        > "$grp_count"
+## parse relevant tool output from logfile to file
+cat mothur.*.logfile
+| head -n-7
+| sed '1,30d'
+> '$grp_count'
     ]]></command>
     <inputs>
         <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/>
@@ -73,14 +73,20 @@
     <tests>
         <test>
             <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
+            <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="source" value="groups"/>
             <param name="groups" value="forest,pasture"/>
             <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
             <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -91,7 +97,7 @@
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _group: https://www.mothur.org/wiki/Group_file
 .. _count.groups: https://www.mothur.org/wiki/Count.groups
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>