--- a/subtractBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/subtractBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,34 +1,32 @@
-<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@">
     <description>remove intervals based on overlaps</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools subtract
-        $strand
-        -a '$inputA'
-        -b '$inputB'
-        -f $overlap
-        $removeIfOverlap
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools subtract
+$strand
+-a '$inputA'
+-b '$inputB'
+@OVERLAP@
+$removeIfOverlap
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="strand2" />
         <expand macro="overlap" />
         <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="" selected="true">Don't 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 (-A)</option>
+            <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature) (-N)</option>
         </param>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -49,8 +47,7 @@
             <output name="output" file="subtractBed_result3.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <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.
@@ -58,7 +55,6 @@
 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>