--- a/uniq.xml	Thu May 15 12:42:00 2014 -0400
+++ b/uniq.xml	Tue Dec 13 03:02:52 2016 -0500
@@ -1,20 +1,25 @@
-<tool id="bg_uniq" name="Unique" version="0.3">
-  <description>occurrences of each record</description>
-  <command interpreter='python'>
-    uniq.py 
-        $ignore_case 
+<tool id="bg_uniq" name="unique" version="0.4">
+    <description>occurrences of each record</description>
+    <requirements>
+        <requirement type="package" version="2.7.12">python</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+    python '$__tool_directory__/uniq.py'
+        $ignore_case
         $is_numeric
         #if $adv_opts.adv_opts_selector=="advanced":
             $adv_opts.column_start
             $adv_opts.column_end
         #end if
-        $outfile
-        $input
+        '$outfile'
+        '$input'
+]]>
   </command>
   <inputs>
-    <param name="input" type="data" format="tabular,text" label="from query" /> 
-    <param name="ignore_case" type="boolean" label="ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/>
-    <param name="is_numeric" type="boolean" label="column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/>
+    <param name="input" type="data" format="tabular,text" label="from query" />
+    <param name="ignore_case" type="boolean" label="Ignore differences in case when comparing" truevalue="-f" falsevalue="false" checked="false" />
+    <param name="is_numeric" type="boolean" label="Column only contains numeric values" truevalue="-n" falsevalue="false" checked="false" />
     <conditional name="adv_opts">
         <param name="adv_opts_selector" type="select" label="Advanced Options">
           <option value="basic" selected="True">Hide Advanced Options</option>
@@ -32,28 +37,44 @@
   </outputs>
   <tests>
     <test>
+      <param name="input" value="1.bed"/>
+      <param name="is_numeric" value="True"/>
+      <param name="ignore_case" value="True"/>
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="column_start" value="2"/>
+      <param name="column_end" value="3"/>
+      <output name="outfile" file="uniq_results1.bed"/>
+    </test>
+    <test>
+      <param name="input" value="1.bed"/>
+      <param name="is_numeric" value="False"/>
+      <param name="ignore_case" value="True"/>
+      <param name="adv_opts_selector" value="advanced"/>
+      <param name="column_start" value="1"/>
+      <param name="column_end" value="1"/>
+      <output name="outfile" file="uniq_results2.bed"/>
     </test>
   </tests>
   <help>
-  
- .. class:: infomark
+<![CDATA[
 
-**Syntax**
+
+**What it does**
 
 This tool returns all unique lines using the 'sort -u' command.
-
------
-
-.. class:: infomark
+    
+**Input**
 
 The input file needs to be tab separated. Please convert your file if necessary.
 
------
+**Output**
 
-**Example**
+This tool returns all unique lines:
+
+Example:
 
 - Input file::
-     
+
        chr1   10  100  gene1
        chr1  105  200  gene2
        chr1   10  100  gene1
@@ -71,5 +92,16 @@
        chr3   15 1656  gene6
 
 
-</help>
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{bgruening_galaxytools,
+                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+                url = {https://github.com/bgruening/galaxytools}
+            }
+        </citation>
+    </citations>
 </tool>