--- a/FileConverter.xml	Mon Feb 12 08:54:03 2018 -0500
+++ b/FileConverter.xml	Wed May 15 06:41:00 2019 -0400
@@ -1,7 +1,7 @@
 <?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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [File Handling]-->
-<tool id="FileConverter" name="FileConverter" version="2.2.0">
+<tool id="FileConverter" name="FileConverter" version="2.3.0">
   <description>Converts between different MS file formats.</description>
   <macros>
     <token name="@EXECUTABLE@">FileConverter</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>FileConverter
+  <command detect_errors="aggressive"><![CDATA[FileConverter
 
 #if $param_in:
   -in $param_in
@@ -44,6 +44,9 @@
     #if $adv_opts.param_force_MaxQuant_compatibility:
   -force_MaxQuant_compatibility
 #end if
+    #if $adv_opts.param_force_TPP_compatibility:
+  -force_TPP_compatibility
+#end if
     #if $adv_opts.param_write_scan_index:
   -write_scan_index
   #if " " in str($adv_opts.param_write_scan_index):
@@ -65,7 +68,7 @@
   -force
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
     <expand macro="advanced_options">
@@ -89,6 +92,7 @@
       <param name="param_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/>
       <param name="param_MGF_compact" display="radio" type="boolean" truevalue="-MGF_compact" falsevalue="" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact) "/>
       <param name="param_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
+      <param name="param_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_compatibility) "/>
       <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
@@ -105,5 +109,5 @@
   <help>Converts between different MS file formats.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileConverter.html</help>
 </tool>