--- a/linksBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/linksBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_links" name="bedtools LinksBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_links" name="bedtools LinksBed" version="@TOOL_VERSION@">
     <description>create a HTML page of links to UCSC locations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools links
-            -base "${basename}"
-            -org "${org}"
-            -db "${db}"
-            -i "${input}"
-            > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools links
+-base '${basename}'
+-org '${org}'
+-db '${db}'
+-i '${input}'
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="basename" type="text" value="http://genome.ucsc.edu"
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="basename" argument="-base" type="text" value="http://genome.ucsc.edu"
             label="The 'basename' for the UCSC genome browser" />
-        <param name="org" type="text" value="human" label="Organism name" help="e.g. mouse, human (-org)" />
-        <param name="db" type="text" value="hg19" label="The genome build" help="(-db)"/>
+        <param argument="-org" type="text" value="human" label="Organism name" help="E.g. mouse, human" />
+        <param argument="-db" type="text" value="hg19" label="The genome build" />
     </inputs>
     <outputs>
         <data name="output" format="html" />
@@ -41,14 +39,12 @@
             <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. This is useful for cases when one wants to manually inspect through a large set of annotations or features.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>