--- a/PeptideIndexer.xml	Mon Feb 12 08:51:00 2018 -0500
+++ b/PeptideIndexer.xml	Wed May 15 05:57:03 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: [ID Processing]-->
-<tool id="PeptideIndexer" name="PeptideIndexer" version="2.2.0">
+<tool id="PeptideIndexer" name="PeptideIndexer" version="2.3.0">
   <description>Refreshes the protein references for all peptide hits.</description>
   <macros>
     <token name="@EXECUTABLE@">PeptideIndexer</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>PeptideIndexer
+  <command detect_errors="aggressive"><![CDATA[PeptideIndexer
 
 #if $param_in:
   -in $param_in
@@ -88,7 +88,8 @@
   -force
 #end if
 #end if
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="idxml" optional="False" label="Input idXML file containing the identifications" help="(-in) "/>
     <param name="param_fasta" type="data" format="fasta" optional="False" label="Input sequence database in FASTA format" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
@@ -119,25 +120,30 @@
     <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
     <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Formic_acid">Formic_acid</option>
       <option value="TrypChymo">TrypChymo</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="Arg-C">Arg-C</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
       <option value="PepsinA">PepsinA</option>
       <option value="Asp-N">Asp-N</option>
-      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Lys-C">Lys-C</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
       <option value="no cleavage">no cleavage</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="V8-E">V8-E</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="V8-DE">V8-DE</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
     </param>
     <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
       <option value="full" selected="true">full</option>
@@ -154,5 +160,5 @@
   <help>Refreshes the protein references for all peptide hits.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PeptideIndexer.html</help>
 </tool>