--- a/unsorted_uniq.xml	Sun Oct 06 08:22:36 2013 -0400
+++ b/unsorted_uniq.xml	Wed Jan 07 11:10:52 2015 -0500
@@ -1,44 +1,57 @@
-<tool id="tp_sorted_uniq" name="Unique" version="0.3">
+<tool id="tp_sorted_uniq" name="Unique" version="@BASE_VERSION@.0">
   <description>occurrences of each record</description>
-    <requirements>
-        <requirement type="package" version="8.21">gnu_coreutils</requirement>
-    </requirements>
-    <command interpreter='python'>
-        unsorted_uniq.py 
-            $ignore_case 
-            $is_numeric
-            #if $adv_opts.adv_opts_selector=="advanced":
-                $adv_opts.column_start
-                $adv_opts.column_end
-            #end if
-            $outfile
-            $infile
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>sort --version | head -n 1</version_command>
+    <command>
+<![CDATA[
+    sort -u
+        $ignore_case
+        $is_numeric
+        -t '	'
+        #if $adv_opts.adv_opts_selector == "advanced":
+            -k$adv_opts.column_start,$adv_opts.column_end
+        #end if
+        -o "$outfile"
+        "$infile"
+]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular,txt" label="File to scan for unique values" /> 
-        <param name="ignore_case" type="boolean" label="ignore differences in case when comparing (-f)" truevalue="-f" falsevalue="false" checked="false"/>
-        <param name="is_numeric" type="boolean" label="column only contains numeric values (-n)" truevalue="-n" falsevalue="false" checked="false" />
+        <param name="infile" type="data" format="tabular" label="File to scan for unique values" />
+        <param name="ignore_case" type="boolean" truevalue="-f" falsevalue="" checked="False"
+            label="Ignore differences in case when comparing" help="(-f)"/>
+        <param name="is_numeric" type="boolean" truevalue="-n" falsevalue="" checked="False"
+            label="Column only contains numeric values" help="(-n)" />
         <conditional name="adv_opts">
             <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
+                <option value="basic" selected="True">Hide Advanced Options</option>
+                <option value="advanced">Show Advanced Options</option>
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="column_start" label="Column start" type="data_column" data_ref="infile" help="Unique on specific column range"/>
-                <param name="column_end" label="Column end" type="data_column" data_ref="infile" help="Unique on specific column range"/>
+                <param name="column_start" type="data_column" data_ref="infile" label="Column start" help="Unique on specific column range"/>
+                <param name="column_end" type="data_column" data_ref="infile" label="Column end" help="Unique on specific column range"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="infile" name="outfile" metadata_source="infile"/>
+        <data format="input" name="outfile" metadata_source="infile"/>
     </outputs>
     <tests>
         <test>
+            <param name="infile" 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="unique_results1.bed"/>
         </test>
     </tests>
     <help>
-
+<![CDATA[
  .. class:: infomark
 
 **Syntax**
@@ -74,6 +87,7 @@
        chr2 1000 1900  gene5
        chr3   15 1656  gene6
 
-
+@REFERENCES@
+]]>
 </help>
 </tool>