--- a/subtractBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/subtractBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,37 +6,51 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
+<![CDATA[
         bedtools subtract
         $strand
         -a $inputA
         -b $inputB
         -f $overlap
         $removeIfOverlap
-        &gt; $output
+        > $output
+]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
         <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
         <expand macro="strand2" />
         <expand macro="overlap" />
-
-        <param name="strand" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Overlaps on either strand</option>
-            <option value="-s">Only overlaps occurring on the **same** strand.</option>
-            <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
-        </param>
-
         <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
             <option value="" selected="True">Dont Remove entire feature on overlap</option>
-            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed.</option>
-            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature).</option>
+            <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option>
+            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option>
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
+        <data format_source="inputA" name="output" metadata_source="inputA"/>
     </outputs>
+    <tests>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <output name="output" file="subtractBed_result1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <param name="overlap" value="0.80" />
+            <output name="output" file="subtractBed_result2.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="subtractBed1.bed" ftype="bed" />
+            <param name="inputB" value="subtractBed2.bed" ftype="bed" />
+            <param name="removeIfOverlap" value="-A" />
+            <output name="output" file="subtractBed_result3.bed" ftype="bed" />
+        </test>
+    </tests>
     <help>
-
+<![CDATA[
 **What it does**
 
 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
@@ -44,6 +58,7 @@
 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
 
 @REFERENCES@
+]]>
     </help>
     <expand macro="citations" />
 </tool>