--- a/mergeBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/mergeBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,60 +6,59 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
-        mergeBed 
-            -i $input
-            $strandedness
-            $report_number
+<![CDATA[
+        mergeBed
+            -i "${input}"
+            $strand
             -d $distance
-            $nms
-            #if str($scores) != 'none'
-                -scores $scores
-            #end if
-            &gt; $output
+            $header
+            > "${output}"
+]]>
     </command>
     <inputs>
-        <param  name="input" format="bed,gff,vcf" type="data" label="Sort the following BED/VCF/GFF file"/>
-        <param name="strandedness" type="boolean" label="Force strandedness." truevalue="-s" falsevalue="" checked="false" 
-            help="That is, only merge features that are the same strand."/>
-        <param name="report_number" type="boolean" label="Report the number of BED entries that were merged." truevalue="-n" falsevalue="" checked="false" 
-            help="1 is reported if no merging occurred."/>
-        <param name="nms" type="boolean" label="Report the names of the merged features separated by commas." truevalue="-nms" falsevalue="" checked="false" 
-            help="1 is reported if no merging occurred."/>
-
-        <param name="distance" type="integer" value="0" label="Maximum distance between features allowed for features to be merged." 
-            help="That is, overlapping and/or book-ended features are merged."/>
-        <param name="scores" type="select" label="Report the scores of the merged features as">
-            <option value="none" selected="True">Do not report at all</option>
-            <option value="sum">Sum</option>
+        <param  name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/>
+        <param name="strand" type="select" label="Calculation based on strandedness?">
+            <option value="" selected="True">Overlaps on either strand</option>
+            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
+            <option value="-S +">Force merge for forward strand only.</option>
+            <option value="-S -">Force merge for reverse strand only.</option>
+        </param>
+        <param name="distance" type="integer" value="0"
+            label="Maximum distance between features allowed for features to be merged"
+            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
+        <expand macro="print_header" />
+        <expand macro="choose_columns" />
+        <expand macro="choose_operations">
             <expand macro="math_options" />
-        </param>
+            <expand macro="additional_math_options" />
+        </expand>
     </inputs>
     <outputs>
         <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="input" value="0.bed" ftype="bed" />
-            <output name="output" file="0_result.bed" ftype="bed" />
+            <param name="input" value="mergedBed1.bed" ftype="bed" />
+            <output name="output" file="mergedBed_result1.bed" ftype="bed" />
         </test>
         <test>
-            <param name="input" value="1.bed" ftype="bed" />
+            <param name="input" value="mergedBed2.bed" ftype="bed" />
             <param name="strandedness" value="-s" />
-            <output name="output" file="1_result.bed" ftype="bed" />
+            <output name="output" file="mergedBed_result2.bed" ftype="bed" />
         </test>
         <test>
-            <param name="input" value="2.bed" ftype="bed" />
+            <param name="input" value="mergedBed3.bed" ftype="bed" />
             <param name="report_number" value="-n" />
-            <output name="output" file="2_result.bed" ftype="bed" />
+            <output name="output" file="mergedBed_result3.bed" ftype="bed" />
         </test>
         <test>
-            <param name="input" value="3.bed" ftype="bed" />
+            <param name="input" value="mergedBed4.bed" ftype="bed" />
             <param name="distance" value="1000" />
-            <output name="output" file="3_result.bed" ftype="bed" />
+            <output name="output" file="mergedBed_result4.bed" ftype="bed" />
         </test>
     </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
@@ -197,8 +196,8 @@
   $ bedtools merge -i A.bed -scores collapse
   chr1  100  500  1,2,3
 
-
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>