--- a/topGO.xml	Mon Oct 15 11:30:04 2018 -0400
+++ b/topGO.xml	Tue Oct 16 10:28:50 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.12">
+<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2018.10.16">
     <description>(Human, Mouse, Rat) (topGO)</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>
@@ -36,6 +36,16 @@
   --barplotoutput='$barplot'
   --dotplotoutput='$dotplot'
   --geneuniverse='$geneuniverse' 
+  --background="$background_genes.background"
+
+  #if $background_genes.background == "true"
+    --background_genes="$background_genes.inputtype.genelist"
+    --background_input_type="$background_genes.inputtype.filetype"
+    #if $background_genes.inputtype.filetype == "file"
+      --background_header="$background_genes.inputtype.header"
+      --background_column="$background_genes.inputtype.column"
+    #end if
+  #end if
 
     ]]></command>
 
@@ -63,6 +73,35 @@
       <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" /> 
     </when>
   </conditional>
+  <conditional name="background_genes">
+    <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs"/>
+    <when value="true">
+      <conditional name="inputtype">
+        <param name="filetype" type="select" label="Select your type of input file" help="The identifiers must be Ensembl gene IDs (e.g : ENSG00000139618). If it is not the case, please use the ID Mapping tool.">
+          <option value="file" selected="true">Input file containing your identifiers</option>
+          <option value="copy_paste">Copy/paste your list of IDs</option> 
+        </param>
+        <when value="copy_paste">
+          <param name="genelist" type="text" label="Enter a list of identifiers">
+            <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="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/>
+          <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter 'c1' for column n°1..)" value="c1"/> 
+          <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file have a header?" /> 
+        </when>
+      </conditional>
+    </when>
+    <when value="false"/>
+  </conditional>
     <param name="geneuniverse" type="select" label="Select a specie">
       <!--option value="org.At.tair.db" >Arabidopsis</option-->
       <option value="org.Ce.eg.db" >Worm (C. elegans)</option>