--- a/summarize_gff.xml	Wed Aug 14 11:24:42 2019 -0400
+++ b/summarize_gff.xml	Thu Aug 15 07:20:12 2019 -0400
@@ -3,18 +3,18 @@
         <requirement type="package">R</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        summarize_gff.R '$inputgff' '$output'
+        Rscript ${__tool_directory__}/summarize_gff.R '$inputgff' '$output' '$group'
     ]]></command>
     <inputs>
       <param type="data" name="inputgff" format="gff3" />
-      <param name="group" type="select" label="select categories to summarize" multiple="true">
-            <option value="Name">Numerical sort</option>
-            <option value="Final_Classification">General numeric sort</option>
-            <option value="seqid">Alphabetical sort</option>
+      <param name="group" type="select" label="select categories to summarize" multiple="true" optional="false">
+            <option value="Name">protein domain name</option>
+            <option value="Final_Classification">Classification</option>
+            <option value="seqid">Sequence ID</option>
       </param>
     </inputs>
     <outputs>
-        <data name="output" format="csv" />
+        <data name="output" format="tabular" />
     </outputs>
     <help><![CDATA[
         TODO: Fill in help.