--- a/MapAlignmentEvaluation.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MapAlignmentEvaluation.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,44 +1,72 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="1.12.0">
-  <description>Evaluates alignment results against a ground truth.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MapAlignmentEvaluation
+<?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="MapAlignmentEvaluation" name="MapAlignmentEvaluation" version="2.0.0">
+    <description>Evaluates alignment results against a ground truth.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MapAlignmentEvaluation</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MapAlignmentEvaluation
 
--in ${param_in}
--gt ${param_gt}
--type ${param_type}
--rt_dev ${param_rt_dev}
--mz_dev ${param_mz_dev}
--int_dev ${param_int_dev}
-${param_use_charge}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_gt:
+  -gt $param_gt
+#end if
+#if $param_type:
+  -type
+  #if &quot; &quot; in str($param_type):
+    &quot;$param_type&quot;
+  #else
+    $param_type
+  #end if
+#end if
+#if $param_rt_dev:
+  -rt_dev $param_rt_dev
+#end if
+#if $param_mz_dev:
+  -mz_dev $param_mz_dev
+#end if
+#if $param_int_dev:
+  -int_dev $param_int_dev
+#end if
+#if $param_use_charge:
+  -use_charge
+#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="consensusXML" optional="False" label="input file: tool" help="(-in)"/>
-    <param name="param_gt" type="data" format="consensusXML" optional="False" label="input file: ground truth" help="(-gt)"/>
-    <param name="param_type" type="select" optional="False" label="Caap Evaluation type" help="(-type)">
-      <option value="precision">precision</option>
-      <option value="recall">recall</option>
-      <option value="F1">F1</option>
-    </param>
-    <param name="param_rt_dev" type="float" value="0.1" label="Maximum allowed deviation of the retention time" help="(-rt_dev)"/>
-    <param name="param_mz_dev" type="float" value="0.1" label="Maximum allowed deviation of m/z" help="(-mz_dev)"/>
-    <param name="param_int_dev" type="float" value="100.0" label="Maximum allowed deviation of Intensity" help="(-int_dev)"/>
-    <param name="param_use_charge" type="boolean" truevalue="-use_charge true" falsevalue="-use_charge false" checked="false" optional="True" label="Use charge criterion when assesing if two features are identical." help="(-use_charge)"/>
-  </inputs>
-  <outputs/>
-  <help>**What it does**
-
-Evaluates alignment results against a ground truth.
+    <inputs>
+      <param format="consensusxml" help="(-in) " label="input file: tool" name="param_in" optional="False" type="data"/>
+      <param format="consensusxml" help="(-gt) " label="input file: ground truth" name="param_gt" optional="False" type="data"/>
+      <param help="(-type) " label="Caap Evaluation type" name="param_type" optional="False" type="select">
+        <option value="precision">precision</option>
+        <option value="recall">recall</option>
+        <option value="F1">F1</option>
+      </param>
+      <param help="(-rt_dev) " label="Maximum allowed deviation of the retention time" name="param_rt_dev" type="float" value="0.1"/>
+      <param help="(-mz_dev) " label="Maximum allowed deviation of m/z" name="param_mz_dev" type="float" value="0.1"/>
+      <param help="(-int_dev) " label="Maximum allowed deviation of Intensity" name="param_int_dev" type="float" value="100.0"/>
+      <param checked="false" falsevalue="" help="(-use_charge) " label="Use charge criterion when assesing if two features are identical" name="param_use_charge" optional="True" truevalue="-use_charge" type="boolean"/>
+      <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>Evaluates alignment results against a ground truth.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MapAlignmentEvaluation.html</help>
+  </tool>