--- a/IDFilter.xml	Mon Feb 12 08:44:17 2018 -0500
+++ b/IDFilter.xml	Wed May 15 05:35:45 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="IDFilter" name="IDFilter" version="2.2.0">
+<tool id="IDFilter" name="IDFilter" version="2.3.0">
   <description>Filters results from protein or peptide identification engines based on different criteria.</description>
   <macros>
     <token name="@EXECUTABLE@">IDFilter</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>IDFilter
+  <command detect_errors="aggressive"><![CDATA[IDFilter
 
 #if $param_in:
   -in $param_in
@@ -181,7 +181,7 @@
   -best:n_to_m_peptide_hits     "$adv_opts.param_best_n_to_m_peptide_hits"
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
     <param name="param_length" type="text" size="30" value=":" label="Keep only peptide hits with a sequence length in this range" help="(-length) ">
@@ -225,7 +225,7 @@
     <param name="param_score_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept" help="(-pep) "/>
     <param name="param_score_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept" help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides"/>
     <param name="param_whitelist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) &lt;br&gt;All peptides that are not referencing a protein in this file are removed. &lt;br&gt;All proteins whose accessions are not present in this file are removed"/>
-    <repeat name="rep_param_whitelist_protein_accessions" min="0" max="1" title="param_whitelist_protein_accessions">
+    <repeat name="rep_param_whitelist_protein_accessions" min="0" title="param_whitelist_protein_accessions">
       <param name="param_whitelist_protein_accessions" type="text" size="30" label="All peptides that do not reference at least one of the provided protein accession are removed" help="(-protein_accessions) &lt;br&gt;Only proteins of the provided list are retained">
         <sanitizer>
           <valid initial="string.printable">
@@ -237,7 +237,7 @@
     </repeat>
     <param name="param_whitelist_peptides" type="data" format="idxml" optional="True" label="Only peptides with the same sequence and modification assignment as any peptide in this file are kept" help="(-peptides) Use with 'whitelist:ignore_modifications' to only compare by sequence. &lt;br&gt;"/>
     <param name="param_whitelist_ignore_modifications" display="radio" type="boolean" truevalue="-whitelist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare whitelisted peptides by sequence only" help="(-ignore_modifications) "/>
-    <repeat name="rep_param_whitelist_modifications" min="0" max="1" title="param_whitelist_modifications">
+    <repeat name="rep_param_whitelist_modifications" min="0" title="param_whitelist_modifications">
       <param name="param_whitelist_modifications" type="select" optional="True" label="Keep only peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) ">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2771,7 +2771,7 @@
       </param>
     </repeat>
     <param name="param_blacklist_proteins" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences" help="(-proteins) &lt;br&gt;All peptides that are referencing a protein in this file are removed. &lt;br&gt;All proteins whose accessions are present in this file are removed"/>
-    <repeat name="rep_param_blacklist_protein_accessions" min="0" max="1" title="param_blacklist_protein_accessions">
+    <repeat name="rep_param_blacklist_protein_accessions" min="0" title="param_blacklist_protein_accessions">
       <param name="param_blacklist_protein_accessions" type="text" size="30" label="All peptides that reference at least one of the provided protein accession are removed" help="(-protein_accessions) &lt;br&gt;Only proteins not in the provided list are retained">
         <sanitizer>
           <valid initial="string.printable">
@@ -2783,7 +2783,7 @@
     </repeat>
     <param name="param_blacklist_peptides" type="data" format="idxml" optional="True" label="Peptides with the same sequence and modification assignment as any peptide in this file are filtered out" help="(-peptides) Use with 'blacklist:ignore_modifications' to only compare by sequence. &lt;br&gt;"/>
     <param name="param_blacklist_ignore_modifications" display="radio" type="boolean" truevalue="-blacklist:ignore_modifications" falsevalue="" checked="false" optional="True" label="Compare blacklisted peptides by sequence only" help="(-ignore_modifications) "/>
-    <repeat name="rep_param_blacklist_modifications" min="0" max="1" title="param_blacklist_modifications">
+    <repeat name="rep_param_blacklist_modifications" min="0" title="param_blacklist_modifications">
       <param name="param_blacklist_modifications" type="select" optional="True" label="Remove all peptides with sequences that contain (any of) the selected modification(s)" help="(-modifications) ">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5318,26 +5318,31 @@
     </repeat>
     <param name="param_digest_fasta" type="data" format="fasta" optional="True" label="Input sequence database in FASTA format" help="(-fasta) "/>
     <param name="param_digest_enzyme" type="select" optional="False" value="Trypsin" label="Specify the digestion enzyme" help="(-enzyme) ">
+      <option value="V8-DE">V8-DE</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Lys-N">Lys-N</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="Formic_acid">Formic_acid</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="V8-E">V8-E</option>
+      <option value="CNBr">CNBr</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
       <option value="Asp-N">Asp-N</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="Trypsin/P">Trypsin/P</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="TrypChymo">TrypChymo</option>
       <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Asp-N/B">Asp-N/B</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="CNBr">CNBr</option>
-      <option value="V8-E">V8-E</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Arg-C">Arg-C</option>
+      <option value="Arg-C/P">Arg-C/P</option>
     </param>
     <param name="param_digest_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the filte" help="(-specificity) ">
       <option value="full" selected="true">full</option>
@@ -5376,5 +5381,5 @@
   <help>Filters results from protein or peptide identification engines based on different criteria.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDFilter.html</help>
 </tool>