--- a/InternalCalibration.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/InternalCalibration.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,53 +1,81 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="InternalCalibration" name="InternalCalibration" version="1.12.0">
-  <description>Applies an internal calibration.</description>
-  <macros>
-    <token name="@EXECUTABLE@">InternalCalibration</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>InternalCalibration
+<?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: [Signal processing and preprocessing]-->
+  <tool id="InternalCalibration" name="InternalCalibration" version="2.0.0">
+    <description>Applies an internal calibration.</description>
+    <macros>
+      <token name="@EXECUTABLE@">InternalCalibration</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>InternalCalibration
 
--in ${param_in}
--out ${param_out}
--ref_peaks ${param_ref_peaks}
--type ${param_type}
--trafo ${param_trafo}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:mz_tolerance ${param_mz_tolerance}
--algorithm:mz_tolerance_unit ${param_mz_tolerance_unit}
--algorithm:rt_tolerance ${param_rt_tolerance}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_ref_peaks:
+  -ref_peaks $param_ref_peaks
+#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_trafo:
+  -trafo $param_trafo
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_algorithm_mz_tolerance:
+  -algorithm:mz_tolerance $param_algorithm_mz_tolerance
+#end if
+#if $param_algorithm_mz_tolerance_unit:
+  -algorithm:mz_tolerance_unit
+  #if &quot; &quot; in str($param_algorithm_mz_tolerance_unit):
+    &quot;$param_algorithm_mz_tolerance_unit&quot;
+  #else
+    $param_algorithm_mz_tolerance_unit
+  #end if
+#end if
+#if $param_algorithm_rt_tolerance:
+  -algorithm:rt_tolerance $param_algorithm_rt_tolerance
+#end if
+#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="mzML,featureXML" optional="False" label="input peak file " help="(-in)"/>
-    <param name="param_ref_peaks" type="data" format="tabular,idXML" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks)"/>
-    <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied." help="(-type)">
-      <option value="spectrumwise">spectrumwise</option>
-      <option value="global">global</option>
-    </param>
-    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z." help="(-mz_tolerance)"/>
-    <param name="param_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance." help="(-mz_tolerance_unit)">
-      <option value="Da">Da</option>
-      <option value="ppm">ppm</option>
-    </param>
-    <param name="param_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt." help="(-rt_tolerance)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file " format="featureXML">
-      <change_format>
-        <when input="param_out_type" value="mzML" format="mzML"/>
-      </change_format>
-    </data>
-    <data name="param_trafo" label="output transformation file (only for global calibration)" format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Applies an internal calibration.
+    <inputs>
+      <param format="xml,mzml" help="(-in) " label="input peak file" name="param_in" optional="False" type="data"/>
+      <param format="tabular,xml" help="(-ref_peaks) " label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" name="param_ref_peaks" optional="True" type="data"/>
+      <param help="(-type) " label="The kind of internal calibration that should be applied" name="param_type" optional="True" type="select" value="spectrumwise">
+        <option value="spectrumwise">spectrumwise</option>
+        <option value="global">global</option>
+      </param>
+      <param help="(-mz_tolerance) " label="Allowed tolerance between peak and reference m/z" min="0.0" name="param_algorithm_mz_tolerance" optional="True" type="float" value="1.0"/>
+      <param help="(-mz_tolerance_unit) " label="Unit for mz_tolerance" name="param_algorithm_mz_tolerance_unit" optional="True" type="select" value="Da">
+        <option value="Da">Da</option>
+        <option value="ppm">ppm</option>
+      </param>
+      <param help="(-rt_tolerance) " label="Allowed tolerance between peak and reference rt" name="param_algorithm_rt_tolerance" type="integer" value="10"/>
+      <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="input" metadata_source="param_in" name="param_out"/>
+      <data format="trafoxml" name="param_trafo"/>
+    </outputs>
+    <help>Applies an internal calibration.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
+  </tool>