--- a/LabeledEval.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/LabeledEval.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,34 +1,51 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="LabeledEval" name="LabeledEval" version="1.12.0">
-  <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
-  <macros>
-    <token name="@EXECUTABLE@">LabeledEval</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>LabeledEval
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Utilities]-->
+  <tool id="LabeledEval" name="LabeledEval" version="2.0.0">
+    <description> Evaluation tool for isotope-labeled quantitation experiments.</description>
+    <macros>
+      <token name="@EXECUTABLE@">LabeledEval</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>LabeledEval
 
--in ${param_in}
--truth ${param_truth}
--rt_tol ${param_rt_tol}
--mz_tol ${param_mz_tol}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_truth:
+  -truth $param_truth
+#end if
+#if $param_rt_tol:
+  -rt_tol $param_rt_tol
+#end if
+#if $param_mz_tol:
+  -mz_tol $param_mz_tol
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+&gt; $param_stdout
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML" optional="False" label="Feature result file" help="(-in)"/>
-    <param name="param_truth" type="data" format="consensusXML" optional="False" label="Expected result file." help="(-truth)"/>
-    <param name="param_rt_tol" type="float" value="20.0" label="Maximum allowed retention time deviation" help="(-rt_tol)"/>
-    <param name="param_mz_tol" type="float" value="0.25" label="Maximum allowed m/z deviation (divided by charge)" help="(-mz_tol)"/>
-  </inputs>
-  <outputs/>
-  <help>**What it does**
-
- Evaluation tool for isotope-labeled quantitation experiments.
+    <inputs>
+      <param format="xml" help="(-in) " label="Feature result file" name="param_in" optional="False" type="data"/>
+      <param format="consensusxml" help="(-truth) " label="Expected result file" name="param_truth" optional="False" type="data"/>
+      <param help="(-rt_tol) " label="Maximum allowed retention time deviation" name="param_rt_tol" type="float" value="20.0"/>
+      <param help="(-mz_tol) " label="Maximum allowed m/z deviation (divided by charge)" name="param_mz_tol" type="float" value="0.25"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="text" label="Output from stdout" name="param_stdout"/>
+    </outputs>
+    <help> Evaluation tool for isotope-labeled quantitation experiments.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LabeledEval.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LabeledEval.html</help>
+  </tool>