--- a/IDExtractor.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDExtractor.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,37 +1,53 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDExtractor" name="IDExtractor" version="1.12.0">
-  <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDExtractor</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDExtractor
+<?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="IDExtractor" name="IDExtractor" version="2.0.0">
+    <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDExtractor</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDExtractor
 
--in ${param_in}
--out ${param_out}
--number_of_peptides ${param_number_of_peptides}
--number_of_rand_invokations ${param_number_of_rand_invokations}
-${param_best_hits}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_number_of_peptides:
+  -number_of_peptides $param_number_of_peptides
+#end if
+#if $param_number_of_rand_invokations:
+  -number_of_rand_invokations $param_number_of_rand_invokations
+#end if
+#if $param_best_hits:
+  -best_hits
+#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="idXML" optional="False" label="input file" help="(-in)"/>
-    <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides)"/>
-    <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations)"/>
-    <param name="param_best_hits" type="boolean" truevalue="-best_hits true" falsevalue="-best_hits false" checked="false" optional="True" label="If this flag is set the best n peptides are chosen." help="(-best_hits)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="idXML"/>
-  </outputs>
-  <help>**What it does**
-
-Extracts 'n' peptides randomly or best 'n' from idXML files.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-number_of_peptides) " label="Number of randomly chosen peptides" min="1" name="param_number_of_peptides" optional="True" type="integer" value="10"/>
+      <param help="(-number_of_rand_invokations) " label="Number of rand invocations before random draw" min="0" name="param_number_of_rand_invokations" optional="True" type="integer" value="0"/>
+      <param checked="false" falsevalue="" help="(-best_hits) " label="If this flag is set the best n peptides are chosen" name="param_best_hits" optional="True" truevalue="-best_hits" 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="xml" name="param_out"/>
+    </outputs>
+    <help>Extracts 'n' peptides randomly or best 'n' from idXML files.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html</help>
+  </tool>