--- a/MSGFPlusAdapter.xml	Mon Feb 12 08:52:43 2018 -0500
+++ b/MSGFPlusAdapter.xml	Wed May 15 06:00:35 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="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.2.0">
+<tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.3.0">
   <description>MS/MS database search using MS-GF+.</description>
   <macros>
     <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command><![CDATA[
+<command detect_errors="aggressive"><![CDATA[
 
  ## check input file type
  #set $in_type = $param_in.ext
@@ -143,13 +143,14 @@
   -force
 #end if
 #end if
-]]>
+-threads "\${GALAXY_SLOTS:-1}"
+ ]]>
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
     <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
-    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
-    <param name="param_precursor_mass_tolerance" type="float" value="20.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
+    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys. Decoys are marked by the prefix XXX_"/>
+    <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
     <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
       <option value="Da">Da</option>
       <option value="ppm" selected="true">ppm</option>
@@ -174,17 +175,17 @@
       <option value="TOF">TOF</option>
       <option value="Q_Exactive">Q_Exactive</option>
     </param>
-    <param name="param_enzyme" type="select" optional="False" value="trypsin" label="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" help="(-enzyme) ">
-      <option value="unspecific">unspecific</option>
-      <option value="trypsin" selected="true">trypsin</option>
-      <option value="chymotrypsin">chymotrypsin</option>
-      <option value="LysC">LysC</option>
-      <option value="LysN">LysN</option>
-      <option value="GluC">GluC</option>
-      <option value="ArgC">ArgC</option>
-      <option value="AspN">AspN</option>
-      <option value="alphaLP">alphaLP</option>
-      <option value="no_cleavage">no_cleavage</option>
+    <param name="param_enzyme" type="select" optional="False" value="Trypsin/P" label="Enzyme used for digestion, or type of cleavage" help="(-enzyme) Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')">
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Trypsin/P" selected="true">Trypsin/P</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
     </param>
     <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) ">
       <option value="none" selected="true">none</option>
@@ -5277,11 +5278,11 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="idxml"/>
-    <data name="param_mzid_out" format="mzid"/>
+    <data name="param_out" format="idxml" label="${tool.name} on ${on_string}: idxml"/>
+    <data name="param_mzid_out" format="mzid" label=" ${tool.name} on ${on_string}: mzid"/>
   </outputs>
   <help>MS/MS database search using MS-GF+.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MSGFPlusAdapter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MSGFPlusAdapter.html</help>
 </tool>