--- a/closestBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/closestBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
     <description>find the closest, potentially non-overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -24,13 +24,15 @@
 #if str($overlap_with.source) == "data_table":
     -b '$overlap_with.table.fields.path'
 #else
-    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB])
-    -b '$inputBs'
+    -b
+    #for $file in $overlap_with.inputB:
+        '$file'
+    #end for
 #end if
 > '$output'
     ]]></command>
     <inputs>
-        <param name="inputA" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <!-- overlap with file (inputB) -->
         <conditional name="overlap_with">
             <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
@@ -46,7 +48,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="inputB" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
+                <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
             </when>
         </conditional>
 
@@ -100,7 +102,7 @@
     </inputs>
     <outputs>
         <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
-        <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
+        <!-- <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
         <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
     </outputs>
     <tests>