--- a/multiIntersectBed.xml	Fri Aug 18 15:32:52 2017 -0400
+++ b/multiIntersectBed.xml	Tue Sep 05 09:51:56 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1">
     <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
@@ -11,10 +11,8 @@
         $header
         $cluster
         -filler "${filler}"
-        #if $zero.value == True:
-            -empty
-            -g $genome
-        #end if
+        $empty.empty_selector
+        @GENOME_FILE_UNION@
 
         #if str($tag.tag_select) == "tag":
             #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
@@ -45,17 +43,23 @@
             <when value="custom">
                 <repeat name="beds" title="Add BED files" min="2" >
                     <param name="input" format="bed" type="data" multiple="True" label="BED file" />
-                    <param name="custom_name" type="text" area="false" label="Custom sample name"/>
+                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
-        <expand macro="genome" />
         <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
             label="Invoke Ryan Layers's clustering algorithm"
             help="(-cluster)" />
-        <param name="zero" type="boolean" checked="true"
-            label="Report regions that are not covered by any of the files"
-            help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" />
+        <conditional name="empty">
+            <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
+                <option value="-empty">Yes</option>
+                <option value="">No</option>
+            </param>
+            <when value="-empty">
+                <expand macro="input_conditional_genome_file" />
+            </when>
+            <when value="" />
+        </conditional>
         <param name="filler" type="text" value="N/A"
             label="Text to use for no-coverage value"
             help="Can be 0.0, N/A, - or any other value. (-filler)" />
@@ -67,23 +71,24 @@
     </outputs>
     <tests>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
-            <param name="zero" value="False"/>
+            <param name="empty_selector" value="" />
             <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
         </test>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
-            <param name="header" value="True"/>
-            <param name="zero" value="False"/>
+            <param name="header" value="True" />
+            <param name="empty_selector" value="" />
             <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
         </test>
         <test>
-            <param name="tag_select" value="tag"/>
+            <param name="tag_select" value="tag" />
             <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
-            <param name="zero" value="True"/>
-            <param name="genome" value="multiIntersectBed1.len"/>
+            <param name="empty_selector" value="-empty" />
+            <param name="genome_file_opts_selector" value="hist" />
+            <param name="genome" value="multiIntersectBed1.len" />
             <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>