--- a/coverageBed.xml	Fri Dec 08 03:26:42 2017 -0500
+++ b/coverageBed.xml	Wed Jan 10 19:21:33 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -7,8 +7,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set inputBs = "' '".join([str($file) for $file in $inputB])
-
         bedtools coverage
         $d
         $hist
@@ -23,14 +21,32 @@
         $reciprocal_overlap
         $a_or_b
         -a '$inputA'
-        -b '$inputBs'
+        #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
+            -b '$reduce_or_iterate.inputB'
+        #else:
+            #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
+            -b '$inputBs'
+        #end if
         | sort -k1,1 -k2,2n
         > '$output'
 ]]>
     </command>
     <inputs>
         <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
-        <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
+        <conditional name="reduce_or_iterate">
+            <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
+                <option value='iterate' selected='true'>One output file per 'input B' file</option>
+                <option value='reduce'>Single output containing results for all 'input B' files</option>
+            </param>
+            <when value='iterate'>
+                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+            </when>
+            <when value='reduce'>
+                <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
+                       label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
+            </when>
+        </conditional>
         <expand macro="split" />
         <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
             help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>