--- a/zinbra.xml	Wed Oct 28 19:52:30 2015 +0300
+++ b/zinbra.xml	Wed Oct 28 20:08:20 2015 +0300
@@ -5,20 +5,36 @@
     </requirements>
     <stdio>
         <!-- Wrapper ensures anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
+        <exit_code range="1:"/>
+        <exit_code range=":-1"/>
     </stdio>
     <command interpreter="python">
-        zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
+        #if $action.selection == "analyze"
+            zinbra.py "${genome}" "${bin}" "${fdr}" analyze "${bed}"
+        #else
+            zinbra.py "${genome}" "${bin}" "${fdr}" compare "${bed1}" "${bed2}"
+        #end if
     </command>
     <inputs>
-        <param name="bed" type="data" format="bed" label="Aligned reads" description="BED Aligned reads to process" />
-        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference" />
-        <param name="bin" size="5" type="integer" value="200" label="Bin size" />
-        <param name="fdr" size="5" type="float" value="0.0001" label="FDR" />
+        <param name="genome" type="data" format="fasta" label="Genome build" description="Genome build reference"/>
+        <param name="bin" size="5" type="integer" value="200" label="Bin size"/>
+        <param name="fdr" size="5" type="float" value="0.0001" label="FDR"/>
+        <conditional name="action">
+            <param name="selection" type="select" label="Action">
+                <option value="analyze">Compute enrichment of ChIP-Seq</option>
+                <option value="compare">Compare different ChIP-Seqs</option>
+            </param>
+            <when value="analyze">
+                <param name="bed" type="data" format="bed" label="ChIP-Seq bed" description="BED Aligned reads to process"/>
+            </when>
+            <when value="compare">
+                <param name="bed1" type="data" format="bed" label="ChIP-Seq bed1" description="BED Aligned reads 1 to process"/>
+                <param name="bed2" type="data" format="bed" label="ChIP-Seq bed2" description="BED Aligned reads 2 to process"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="result" format="bed" label="result.bed" />
+        <data name="result" format="bed" label="result.bed"/>
     </outputs>
     <help>
 Zinbra is a tool for analyzing and comparing ChIP-Seq data using Zero Inflated Negative Binomial Restricted Algorithm.