--- a/tagBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/tagBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,46 +6,50 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
+        #set files = '" "'.join( [ str( $file ) for $file in $inputB ] )
         bedtools tag
-        -i $inputA
-        -files 
-        #for $bed in beds:
-            $bed.input
-        #end for
+        -i "${inputA}"
+        -files "${files}"
         -f $overlap
         $strand
-        -tag $tag
+        -tag "${tag}"
         $field
-        &gt; $output
+        > "${output}"
+]]>
     </command>
     <inputs>
-        <param format="bam" name="inputA" type="data" label="BAM file"/>
-
-        <repeat name="beds" title="Add files" >
-            <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file" />
-        </repeat>
+        <param name="inputA" format="bam" type="data" label="BAM file"/>
+        <param name="inputB" format="bed,gff,vcf" multiple="True" type="data" label="BED/VCF/GFF file" />
         <expand macro="strand2" />
         <expand macro="overlap" />
-        
-        <param name="tag" type="text" value="YB" label="Dictate what the tag should be." />
-        <param name="field" type="select" label="Use which field from the annotation files to populate tags?">
-            <option value="-labels" selected="True">labels</option>
+        <param name="tag" type="text" value="YB" label="Specify the tag to use" />
+        <param name="field" type="select" label="Field from the annotation files to populate tags?">
+            <option value="-labels" selected="True">Labels</option>
             <option value="-scores">Scores</option>
             <option value="-names">Names</option>
             <option value="-labels -intervals">Intervals</option>
         </param>
     </inputs>
     <outputs>
-        <data format="bed" name="output" label="" />
+        <data format="bam" name="output"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="srma_in3.bam" ftype="bam" />
+            <param name="inputB" value="tagBed1.bed" ftype="bed" />
+            <param name="field" value="-names" />
+            <output name="output" file="tagBed_result1.bam" ftype="bam" />
+        </test>
+    </tests>
     <help>
-    
+<![CDATA[
 **What it does**
 
 Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in an input bam file
 
 @REFERENCES@
-
+]]>
     </help>
     <expand macro="citations" />
 </tool>