--- a/annotateBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/annotateBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,23 +6,28 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools annotate
-        -i $inputA
-        -files 
-        #for $bed in $names.beds:
-            $bed.input
-        #end for
+        -i "${inputA}"
+        #if $names.names_select == 'yes':
+            -files
+            #for $bed in $names.beds:
+                "${bed.input}"
+            #end for
 
-        #if $names.names_select == 'yes':
             -names
             #for $bed in $names.beds:
-                $bed.inputName
+                "${bed.inputName}"
             #end for
+        #else:
+            #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
+            -files "${files}"
         #end if
         $strand
         $counts
         $both
-        &gt; $output
+        > "${output}"
+]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
@@ -39,28 +44,36 @@
                 </repeat>
             </when>
             <when value="no">
-                <repeat name="beds" title="Add BED files" >
-                    <param name="input" format="bed" type="data" label="BED file" />
-                </repeat>
+                <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
             </when>
         </conditional>
-        
         <expand macro="strand2" />
-        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of -i covered by each file." />
-        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue="" label="Report the count of features followed by the % coverage for each annotation file. Default is to report solely the fraction of the input file covered by each file." />
+        <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
+            label="Report the count of features followed by the % coverage for each annotation file" 
+            help="Default is to report solely the fraction of -i covered by each file." />
+        <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
+            label="Report the count of features followed by the % coverage for each annotation file" 
+            help="Default is to report solely the fraction of the input file covered by each file." />
     </inputs>
-
     <outputs>
-        <data format="bed" name="output" label="" />
+        <data format="bed" name="output" />
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="annotateBed1.bed" ftype="bed" />
+            <param name="names_select" value="no" />
+            <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
+            <output name="output" file="annotateBed_result.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-    
+<![CDATA[
 **What it does**
 
 bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
 
 @REFERENCES@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>