--- a/XTandemAdapter.xml	Mon Feb 12 08:42:13 2018 -0500
+++ b/XTandemAdapter.xml	Wed May 15 05:28:28 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: [Identification]-->
-<tool id="XTandemAdapter" name="XTandemAdapter" version="2.2.0.1">
+<tool id="XTandemAdapter" name="XTandemAdapter" version="2.3.0">
   <description>Annotates MS/MS spectra using X! Tandem.</description>
   <macros>
     <token name="@EXECUTABLE@">XTandemAdapter</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>XTandemAdapter
+  <command detect_errors="aggressive"><![CDATA[XTandemAdapter
 -xtandem_executable xtandem
 
 #if $param_in:
@@ -114,7 +114,7 @@
   -force
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing MS2 spectra" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="FASTA file or pro file" help="(-database) Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir'"/>
@@ -132,7 +132,7 @@
     </param>
     <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/>
     <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/>
-    <repeat name="rep_param_fixed_modifications" min="0"  title="param_fixed_modifications">
+    <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
       <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5200,24 +5200,29 @@
     </repeat>
     <param name="param_minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment mz" help="(-minimum_fragment_mz) "/>
     <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="CNBr">CNBr</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="Trypsin/P">Trypsin/P</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="Asp-N">Asp-N</option>
       <option value="Arg-C">Arg-C</option>
-      <option value="V8-E">V8-E</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
       <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="V8-E">V8-E</option>
     </param>
     <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>
     <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>
@@ -5238,5 +5243,5 @@
   <help>Annotates MS/MS spectra using X! Tandem.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_XTandemAdapter.html</help>
 </tool>