--- a/linksBed.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/linksBed.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -6,29 +6,49 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
-        linksBed
-        -base $basename
-        -org $org
-        -db $db
-        -i $inputA
-        &gt; $output
+<![CDATA[
+        bedtools links
+            -base "${basename}"
+            -org "${org}"
+            -db "${db}"
+            -i "${input}"
+            > "${output}"
+]]>
     </command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param name="basename" type="text" value="http://genome.ucsc.edu" label="The “basename” for the UCSC browser" />
-        <param name="org" type="text" value="human" label="The organism (e.g. mouse, human)" />
-        <param name="db" type="text" value="hg18" label="The genome build" />
+        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file"/>
+        <param name="basename" 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)"/>
     </inputs>
     <outputs>
         <data name="output" format="html" />
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="linksBed1.bed" ftype="bed" />
+            <param name="basename" value="http://genome.ucsc.edu" />
+            <param name="org" value="" />
+            <param name="db" value="" />
+            <output name="output" file="linksBed_result1.html" lines_diff="2" ftype="html" />
+        </test>
+        <test>
+            <param name="input" value="linksBed1.bed" ftype="bed" />
+            <param name="basename" value="http://genome.ucsc.edu" />
+            <param name="org" value="mouse" />
+            <param name="db" value="mm9" />
+            <output name="output" file="linksBed_result2.html" lines_diff="2" ftype="html" />
+        </test>
+    </tests>
     <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>
     <expand macro="citations" />
 </tool>