--- a/coverageBed.xml	Tue Sep 05 15:40:14 2017 -0400
+++ b/coverageBed.xml	Sat Oct 21 07:57:53 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,14 @@
         $hist
         $split
         $strandedness
+        #if str($overlap_a) != "None" and str($overlap_a):
+          -f '$overlap_a'
+        #end if
+        #if str($overlap_b) != "None" and str($overlap_b):
+          -F '$overlap_b'
+        #end if
+        $reciprocal_overlap
+        $a_or_b
         -a '$inputA'
         -b '$inputBs'
         | sort -k1,1 -k2,2n
@@ -32,6 +40,26 @@
         <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
             label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
             help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
+        <param name="overlap_a" type="text"
+            label="Minimum overlap required as a fraction of A."
+            help="Default is 1E-9 (i.e., 1bp). (-f)">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits"><add value=",."/></valid>
+            </sanitizer>
+	</param>
+        <param name="overlap_b" type="text"
+            label="Minimum overlap required as a fraction of B."
+            help="Default is 1E-9 (i.e., 1bp). (-F)">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits"><add value=",."/></valid>
+            </sanitizer>
+	</param>
+        <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
+            label="Require that the fraction overlap be reciprocal for A AND B."
+            help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
+        <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue=""
+            label="Require that the minimum fraction be satisfied for A OR B."
+            help="if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of  B is covered. Without -e, both fractions would have to be satisfied. (-e)" />
     </inputs>
     <outputs>
         <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
@@ -39,9 +67,22 @@
     <tests>
         <test>
             <param name="inputA" value="coverageBedA.bed" ftype="bed" />
-            <param name="genome" value="coverageBedB.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
             <output name="output" file="coverageBed_result1.bed" ftype="bed" />
         </test>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
+            <param name="overlap_b" value="1"  />
+            <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="coverageBedA.bed" ftype="bed" />
+            <param name="inputB" value="coverageBedB.bed" ftype="bed" />
+            <param name="overlap_a" value="1"  />
+            <param name="reciprocal_overlap" value="true"  />
+            <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
+        </test>
     </tests>
     <help>
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