--- a/IDRTCalibration.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDRTCalibration.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,39 +1,57 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDRTCalibration" name="IDRTCalibration" version="1.12.0">
-  <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDRTCalibration</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDRTCalibration
+<?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: [ID Processing]-->
+  <tool id="IDRTCalibration" name="IDRTCalibration" version="2.0.0">
+    <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDRTCalibration</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDRTCalibration
 
--in ${param_in}
--out ${param_out}
--calibrant_1_reference ${param_calibrant_1_reference}
--calibrant_2_reference ${param_calibrant_2_reference}
--calibrant_1_input ${param_calibrant_1_input}
--calibrant_2_input ${param_calibrant_2_input}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_calibrant_1_reference:
+  -calibrant_1_reference $param_calibrant_1_reference
+#end if
+#if $param_calibrant_2_reference:
+  -calibrant_2_reference $param_calibrant_2_reference
+#end if
+#if $param_calibrant_1_input:
+  -calibrant_1_input $param_calibrant_1_input
+#end if
+#if $param_calibrant_2_input:
+  -calibrant_2_input $param_calibrant_2_input
+#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_calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file." help="(-calibrant_1_reference)"/>
-    <param name="param_calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file." help="(-calibrant_2_reference)"/>
-    <param name="param_calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file. Please note that this value needs to be set. The default value -1.0 is not allowed." help="(-calibrant_1_input)"/>
-    <param name="param_calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file. Please note that this value needs to be set. The default value -1.0 is not allowed." help="(-calibrant_2_input)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file " format="idXML"/>
-  </outputs>
-  <help>**What it does**
-
-Can be used to calibrate RTs of peptide hits linearly to standards.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-calibrant_1_reference) " label="The RT of the first calibrant in the reference file" name="param_calibrant_1_reference" type="float" value="0.1"/>
+      <param help="(-calibrant_2_reference) " label="The RT of the second calibrant in the reference file" name="param_calibrant_2_reference" type="float" value="0.9"/>
+      <param help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed" label="The RT of the first calibrant in the input file" name="param_calibrant_1_input" type="float" value="-1.0"/>
+      <param help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed" label="The RT of the second calibrant in the input file" name="param_calibrant_2_input" type="float" value="-1.0"/>
+      <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>Can be used to calibrate RTs of peptide hits linearly to standards.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html</help>
+  </tool>