--- a/cluster_profiler.xml	Wed Sep 05 09:34:57 2018 -0400
+++ b/cluster_profiler.xml	Mon Sep 17 10:30:30 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.05">
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.17">
     <description>
     GO terms classification and enrichment analysis
     </description>
@@ -6,6 +6,7 @@
         <requirement type="package" version="3.4.1">R</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
         <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.Rn.eg.db</requirement>
         <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
         <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
     </requirements>
@@ -37,24 +38,23 @@
             --pval_cutoff="$ego.pval"
             --qval_cutoff="$ego.qval"
             #if $ego.universe.universe_option == "true"
-            #if $ego.universe.universe_input.universe_ids == "text"
-                --universe_type="text"
-                --universe="$ego.universe.universe_input.txt"
-            #else
-                --universe_type="file"
-                --universe="$ego.universe.universe_input.file"
-                --uncol="$ego.universe.universe_input.ncol"
-                --uheader="$ego.universe.universe_input.header"
+                #if $ego.universe.universe_input.universe_ids == "text"
+                    --universe_type="text"
+                    --universe="$ego.universe.universe_input.txt"
+                #else
+                    --universe_type="file"
+                    --universe="$ego.universe.universe_input.file"
+                    --uncol="$ego.universe.universe_input.ncol"
+                    --uheader="$ego.universe.universe_input.header"
+                #end if
+                --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
             #end if
-            --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
-        #end if
         #else
             --go_enrich="false"
         #end if
         
-        --onto_opt="$ontology"
-
-        --text_output="$text_output"
+        --plot="$plot"        
+        --onto_opt="$ontology" > $log
     ]]></command>
     <inputs>
         <conditional name="input" >
@@ -92,7 +92,7 @@
         <param name="species" type="select" label="Select a species" >
             <option value="org.Hs.eg.db">Human</option>
             <option value="org.Mm.eg.db">Mouse</option>
-            <!--option value="org.Sc.eg.db">Rat</option-->
+            <option value="org.Rn.eg.db">Rat</option>
         </param>
         <conditional name="ggo">
             <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>
@@ -151,20 +151,26 @@
             <when value="false"/>
         </conditional>
 				
-		<param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
+		<param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category" optional="false">
             <option value="CC">Cellular Component</option>
             <option value="BP">Biological Process</option>
             <option value="MF">Molecular Function</option>
         </param>
 	    
-	    
+	    <param name="plot" type="select" display="checkboxes" multiple="true" label="Please select your visualization for enrichment analysis" optional="false">
+            <option selected = "true" value="dotplot">dot-plot</option>
+            <option value="barplot">bar-plot</option>
+        </param>
 	    
     </inputs>
     <outputs>
-        <data name="text_output" format="tabular" label="clusterProfiler text output" />
-        <collection type="list" label="clusterProfiler diagram outputs" name="output" >
-	    <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
-	</collection>
+        <data name="log" format="tabular" label="log file" />
+        <collection type="list" label="clusterProfiler text files" name="text_output">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+\.csv)" ext="csv"/>
+        </collection>
+        <collection type="list" label="clusterProfiler diagram outputs" name="graph_output" >
+	        <discover_datasets pattern="(?P&lt;designation&gt;.+plot)" ext="png" />
+	    </collection>
     </outputs>
     <tests>
         <test>
@@ -186,8 +192,8 @@
                 <param name="go_enrich" value="false"/>
             </conditional>
             <param name="ontology" value="CC"/>
-            <output name="text_output" file="clusterProfiler_text_output.tabular"/>
-            <output_collection name="output">
+            <output name="log" />
+            <output_collection name="text_output">
                 <element name="GGO.CC.png" file="GGO.CC.png" ftype="png"/>
             </output_collection>
         </test>