--- a/multiIntersectBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/multiIntersectBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,36 +1,35 @@
-<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@WRAPPER_VERSION@">
+<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
     <description>identifies common intervals among multiple interval files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools multiinter
-        $header
-        $cluster
-        -filler "${filler}"
-        $empty.empty_selector
-        @GENOME_FILE_UNION@
+    <command><![CDATA[
+bedtools multiinter
+$header
+$cluster
+-filler '${filler}'
+$empty.empty_selector
+@GENOME_FILE_UNION@
 
-        #if str($tag.tag_select) == "tag":
-            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
-            -i "${files}"
-        #else:
-            -i
-            #for $file in $tag.beds:
-                "${file.input}"
-            #end for
-            -names
-            #for $file in $tag.beds:
-                "{$file.custom_name}"
-            #end for
-        #end if
-
-        > '$output'
-]]>
-    </command>
+#if str($tag.tag_select) == "tag":
+    -i
+    #for $file in $tag.inputs
+        '$file'
+    #end for
+#else:
+    -i
+    #for $file in $tag.beds:
+        '${file.input}'
+    #end for
+    -names
+    #for $file in $tag.beds:
+        '{$file.custom_name}'
+    #end for
+#end if
+> '$output'
+    ]]></command>
     <inputs>
         <conditional name="tag">
             <param name="tag_select" type="select" label="Sample name">
@@ -38,18 +37,17 @@
                 <option value="custom">Enter custom name per file</option>
             </param>
             <when value="tag">
-                <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
+                <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
             </when>
             <when value="custom">
                 <repeat name="beds" title="Add BED files" min="2" >
-                    <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
+                    <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                     <param name="custom_name" type="text" area="false" label="Custom sample name" />
                 </repeat>
             </when>
         </conditional>
-        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
-            label="Invoke Ryan Layers's clustering algorithm"
-            help="(-cluster)" />
+        <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
+            label="Invoke Ryan Layers's clustering algorithm" />
         <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>
@@ -60,14 +58,13 @@
             </when>
             <when value="" />
         </conditional>
-        <param name="filler" type="text" value="N/A"
+        <param argument="-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)" />
+            help="Can be 0.0, N/A, - or any other value" />
         <expand macro="print_header" />
-
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -92,8 +89,7 @@
             <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
@@ -179,7 +175,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>