--- a/annotate_peak/annotatePeak.xml	Thu Mar 16 16:13:45 2017 -0400
+++ b/annotate_peak/annotatePeak.xml	Mon Mar 20 06:51:22 2017 -0400
@@ -5,11 +5,32 @@
 <stdio>
    <exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoPeakTable"</command>
+<command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData"  "$bindingType"  "$upstream" "$downstream" "$ignore.peak.strand" "$annoPeakTable"</command>
   <inputs>
     <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
       <validator type="empty_field" message="This field is required."/>
     </param>
+    <param name="annoData" type="select" display="radio" label="annoData" help="choose your annoData human or mice">
+      <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option>
+      <option name="mice" type="float" value="">Mice</option>
+    </param>
+    <param name="bindingType" type="select" display="radio" label="bindingType" help="choose bindingType">
+      <option name="sS" type="text" value="startSite">startSite</option>
+      <option name="eS" type="text" value="endSite">endSite</option>
+      <option name="fR" type="text" value="fullRange">fullRange</option>
+    </param>
+    <param name="ignore.peak.strand" type="select" display="radio" label="ignore.peak.strand" help="choose TRUE or FALSE">
+      <option name="T" type="text" value="TRUE">true</option>
+      <option name="F" type="text" value="FALSE">false</option>
+    </param>
+    <param name="upstream" type="float" value=""
+	       label="upstream - number no bigger than 0"
+	       help="e.g. '-5000'" >
+      </param>
+      <param name="downstream" type="float" value=""
+      	       label="downstream - number no less than 1"
+      	       help="e.g. '5000'" >
+            </param>
   </inputs>
   <outputs>
     <data format="csv" name="annoPeakTable" label="peakAnno.csv"/>