--- a/fisherBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/fisherBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,37 +1,35 @@
-<tool id="bedtools_fisher" name="bedtools FisherBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_fisher" name="bedtools FisherBed" version="@TOOL_VERSION@+galaxy1">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools fisher
-        $strand
-        $split
-        -a '$inputA'
-        -b '$inputB'
-        -f $overlap
-        -g @GENOME_FILE@
-        $reciprocal
-        $m
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools fisher
+$strand
+$split
+-a '$inputA'
+-b '$inputB'
+@OVERLAP@
+-g @GENOME_FILE@
+$reciprocal
+$m
+> '$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="input_conditional_genome_file" />
         <expand macro="strand2" />
         <expand macro="split" />
         <expand macro="overlap" />
         <expand macro="reciprocal" />
-        <param name="m" type="boolean" checked="False" truevalue="-m" falsevalue=""
-            label="Merge overlapping intervals before looking at overlap" help="(-m)" />
+        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false"
+            label="Merge overlapping intervals before looking at overlap" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="inputA" format_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Fisher Test on ${inputA.name} and ${inputB.name}"/>
     </outputs>
     <tests>
         <test>
@@ -42,14 +40,12 @@
             <output name="output" file="fisherBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Perform fisher’s exact test on the number of overlaps/unique intervals between 2 files.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>