--- a/macros.xml	Tue Nov 20 10:34:42 2018 -0500
+++ b/macros.xml	Tue Dec 11 14:01:26 2018 -0500
@@ -1,12 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.27.0">bedtools</requirement>
+            <requirement type="package" version="@WRAPPER_VERSION@">bedtools</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.27.0</token>
-    <token name="@SAMTOOLS_VERSION@">1.2</token>
+    <token name="@WRAPPER_VERSION@">2.27.1</token>
+    <token name="@SAMTOOLS_VERSION@">1.9</token>
     <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf</token>
     <token name="@STD_BEDTOOLS_INPUT_LABEL@">bed,bedgraph,gff,vcf</token>
     <xml name="stdio">
@@ -21,12 +21,16 @@
         <version_command>bedtools --version</version_command>
     </xml>
     <xml name="reciprocal">
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
-            label="Require that the fraction of overlap be reciprocal for A and B"
-            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />
+        <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
+            <option value="" selected="True">No</option>
+            <option value="-r">Yes</option>
+        </param>
     </xml>
     <xml name="overlap">
-        <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp. (-f)"/>
+        <param name="overlap" argument="-f" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/>
+    </xml>
+    <xml name="overlapB">
+        <param name="overlapB" argument="-F" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp."/>
     </xml>
     <xml name="strand2">
         <param name="strand" type="select" label="Calculation based on strandedness?">