--- a/cluster_profiler.xml	Fri Mar 23 10:01:41 2018 -0400
+++ b/cluster_profiler.xml	Thu Mar 29 11:43:28 2018 -0400
@@ -36,6 +36,18 @@
             --go_enrich="true"
             --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="$ego.universe.universe_input.header"
+            #end if
+            --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
+        #end if
         #else
             --go_enrich="false"
         #end if
@@ -76,6 +88,7 @@
             <when value="Uniprot"/>
             <when value="Entrez"/>
         </conditional>
+            
         <param name="species" type="select" label="Select a species" >
             <option value="human">Human</option>
             <option value="mouse">Mouse</option>
@@ -97,6 +110,43 @@
             <when value="true">
                 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
 			    <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
+                <conditional name="universe" >
+                    <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs?"/>
+                    <when value="true">
+                        <conditional name="universe_input">
+                            <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list from a file (e.g. table)" >
+                                <option value="text">Copy/paste your background identifiers</option>
+                                <option value="file" selected="true">Input file containing your background identifiers</option>
+                            </param>
+                            <when value="text" >
+                                <param name="txt" type="text" label="Copy/paste your background identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                                    <sanitizer>
+                                        <valid initial="string.printable">
+                                            <remove value="&apos;"/>
+                                        </valid>
+                                        <mapping initial="none">
+                                            <add source="&apos;" target="__sq__"/>
+                                        </mapping>
+                                    </sanitizer>
+                                </param>
+                            </when>
+                            <when value="file" >
+                                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" />
+                                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+                                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                            </when>
+                        </conditional>
+                        <conditional name="universe_idti" >
+                            <param name="universe_idtypein" type="select" label="Select type/source of background identifier of your list" help="Please see example of IDs in help section" >
+                                <option value="Uniprot">UniProt accession number</option>
+                                <option value="Entrez">Entrez Gene ID</option>
+                            </param>
+                            <when value="Uniprot"/>
+                            <when value="Entrez"/>
+                        </conditional>
+                    </when>
+                    <when value="false"/>
+                </conditional>
             </when>
             <when value="false"/>
         </conditional>