--- a/clusterBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/clusterBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,29 +1,27 @@
-<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_clusterbed" name="bedtools ClusterBed" version="@TOOL_VERSION@">
     <description>cluster overlapping/nearby intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools cluster
-        $strand
-        -d $distance
-        -i '$inputA'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools cluster
+$strand
+-d $distance
+-i '$inputA'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Force strandedness."
+        <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness."
             help="That is, only cluster features that are the same strand. By default, this is disabled." />
-        <param name="distance" type="integer" value="0"
+        <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be clustered"
             help="Default is 0. That is, overlapping and/or book-ended features are clustered." />
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA"/>
+        <data name="output" format_source="inputA" metadata_source="inputA"/>
     </outputs>
     <tests>
         <test>
@@ -31,8 +29,7 @@
             <output name="output" file="clusterBed_result.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Similar to merge, cluster report each set of overlapping or “book-ended” features in an interval file. In contrast to merge, cluster does not flatten the cluster of intervals into a new meta-interval; instead, it assigns an unique cluster ID to each record in each cluster. This is useful for having fine control over how sets of overlapping intervals in a single interval file are combined.
@@ -44,7 +41,6 @@
 bedtools cluster requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2n in.bed > in.sorted.bed for BED files).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>