--- a/MapStatistics.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MapStatistics.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,44 +1,57 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MapStatistics" name="MapStatistics" version="1.12.0">
-  <description>Extract extended statistics on the features of a map for quality control.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MapStatistics</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MapStatistics
+<?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: [File Handling]-->
+  <tool id="MapStatistics" name="MapStatistics" version="2.0.0">
+    <description>Extract extended statistics on the features of a map for quality control.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MapStatistics</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MapStatistics
 
--in ${param_in}
--in_type ${param_in_type}
--out ${param_out}
--n ${param_n}
-${param_m}
-${param_p}
-${param_s}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_n:
+  -n $param_n
+#end if
+#if $param_m:
+  -m
+#end if
+#if $param_p:
+  -p
+#end if
+#if $param_s:
+  -s
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Input file" help="(-in)"/>
-    <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content" help="(-in_type)">
-      <option value="featureXML">featureXML</option>
-      <option value="consensusXML">consensusXML</option>
-    </param>
-    <param name="param_n" type="integer" min="1" max="100" optional="True" value="4" label="Report separate statistics for each of n RT slices of the map." help="(-n)"/>
-    <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/>
-    <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/>
-    <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a summary statistics of intensities, qualities, and widths" help="(-s)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Optional output txt file. If '-' or left out, the output is written to the command line." format="txt"/>
-  </outputs>
-  <help>**What it does**
-
-Extract extended statistics on the features of a map for quality control.
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
+      <param help="(-n) " label="Report separate statistics for each of n RT slices of the map" max="100" min="1" name="param_n" optional="True" type="integer" value="4"/>
+      <param checked="false" falsevalue="" help="(-m) " label="Show meta information about the whole experiment" name="param_m" optional="True" truevalue="-m" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-p) " label="Shows data processing information" name="param_p" optional="True" truevalue="-p" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-s) " label="Computes a summary statistics of intensities, qualities, and widths" name="param_s" optional="True" truevalue="-s" 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="txt" name="param_out"/>
+    </outputs>
+    <help>Extract extended statistics on the features of a map for quality control.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapStatistics.html</help>
+  </tool>