--- a/merge.groups.xml	Tue Sep 05 17:01:08 2017 -0400
+++ b/merge.groups.xml	Tue Mar 20 21:56:48 2018 -0400
@@ -7,39 +7,48 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$group" group.dat &&
-        #if $design.source == "hist":
-            ln -s "$design.design_dataset" design_dataset.dat &&
-        #else:
-            ln -s "$generated_design" generated_design.dat &&
-        #end if
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$group' group.dat &&
+ln -s '$fasta' fasta.dat &&
+#if $design.source == "hist":
+    ln -s '$design.design_dataset' design_dataset.dat &&
+#else:
+    ln -s '$generated_design' generated_design.dat &&
+#end if
 
-        echo 'merge.groups(
-            #if $design.source == "hist":
-                design=design_dataset.dat
-            #else:
-                design=generated_design.dat
-            #end if
-            #if $otu:
-                ,shared=otu.dat
-            #end if
-            #if $group:
-                ,group=group.dat
-            #end if
-            #if $groups:
-                ,groups=${ str($groups).replace(",","-") }
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'merge.groups(
+    #if $design.source == "hist":
+        design=design_dataset.dat
+    #else:
+        design=generated_design.dat
+    #end if
+    #if $otu:
+        ,shared=otu.dat
+    #end if
+    #if $group:
+        #if $group.is_of_type("mothur.groups"):
+            ,group=group.dat
+        #elif $group.is_of_type("mothur.count_table"):
+            ,count=group.dat
+        #end if
+    #end if
+    #if $fasta:
+        ,fasta=fasta.dat
+    #end if
+    #if $groups:
+        ,groups=${ str($groups).replace(",","-") }
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    ,method=$method
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <configfiles>
         <configfile name="generated_design"><![CDATA[
@@ -60,12 +69,18 @@
         <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
             <expand macro="labeloptions"/>
         </param>
-        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/>
+        <param name="group" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count - Group Dataset or Count Table"/>
+        <param name="fasta" type="data" format="fasta,mothur.align" optional="true" label="Fasta file" help="only valid if you supplied a count file"/>
         <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
             <options>
                 <filter type="data_meta" ref="otu" key="groups"/>
             </options>
         </param>
+        <param name="method" type="select" label="Merging method">
+            <option value="sum" selected="true"> Sum </option>
+            <option value="average"> Average </option>
+            <option value="median"> Median </option>
+        </param>
         <conditional name="design">
             <param name="source" type="select" label="Grouping Design from" help="">
                 <option value="hist">Your History</option>
@@ -85,6 +100,7 @@
                 </repeat>
             </when>
         </conditional>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -101,6 +117,7 @@
             <param name="source" value="hist"/>
             <param name="design_dataset" value="toymothur.design2"/>
             <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with shared file and label and group select -->
@@ -110,6 +127,7 @@
             <param name="source" value="hist"/>
             <param name="design_dataset" value="toymothur.design2"/>
             <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group file -->
@@ -117,6 +135,23 @@
             <param name="source" value="hist"/>
             <param name="design_dataset" value="toymothur.design2"/>
             <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with count table and fasta file -->
+            <param name="group" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="method" value="median"/>
+            <param name="source" value="hist"/>
+            <param name="design_dataset" value="toymothur.design2"/>
+            <output name="merged_group" ftype="mothur.groups">
+                <assert_contents>
+                    <has_text text="U68589"/>
+                    <has_text text="tardis"/>
+                    <has_text text="dalek"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with design creation -->
@@ -131,11 +166,11 @@
                 <param name="groups" value="pasture"/>
             </repeat>
             <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -156,7 +191,7 @@
 
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>