--- a/RNPxlSearch.xml	Thu Jan 11 18:03:03 2018 -0500
+++ b/RNPxlSearch.xml	Mon Feb 12 13:12:23 2018 -0500
@@ -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: [Utilities]-->
-<tool id="RNPxlSearch" name="RNPxlSearch" version="2.2.0">
+<tool id="RNPxlSearch" name="RNPxlSearch" version="2.3.0">
   <description>Annotate RNA to peptide crosslinks in MS/MS spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">RNPxlSearch</token>
@@ -41,6 +41,17 @@
 #if $param_precursor_max_charge:
   -precursor:max_charge $param_precursor_max_charge
 #end if
+
+#if $rep_param_precursor_isotopes:
+-precursor:isotopes
+  #for token in $rep_param_precursor_isotopes:
+    #if " " in str(token):
+      "$token.param_precursor_isotopes"
+    #else
+      $token.param_precursor_isotopes
+    #end if
+  #end for
+#end if
 #if $param_fragment_mass_tolerance:
   -fragment:mass_tolerance $param_fragment_mass_tolerance
 #end if
@@ -189,12 +200,22 @@
     </param>
     <param name="param_precursor_min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help="(-min_charge) "/>
     <param name="param_precursor_max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help="(-max_charge) "/>
+    <repeat name="rep_param_precursor_isotopes" min="0" max="1" title="param_precursor_isotopes">
+      <param name="param_precursor_isotopes" type="text" size="30" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(-isotopes) (E.g.: 1 = prec. may be misassigned to first isotopic peak)">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_fragment_mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help="(-mass_tolerance) "/>
     <param name="param_fragment_mass_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of fragment m" help="(-mass_tolerance_unit) ">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
     </param>
-    <repeat name="rep_param_modifications_fixed" min="0" max="1" title="param_modifications_fixed">
+    <repeat name="rep_param_modifications_fixed" min="0" title="param_modifications_fixed">
       <param name="param_modifications_fixed" type="select" optional="True" label="Fixed modifications, specified using UniMod (www.unimod.org) terms," help="(-fixed) e.g. 'Carbamidomethyl (C)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -2727,7 +2748,7 @@
         <option value="trifluoro (L)">trifluoro (L)</option>
       </param>
     </repeat>
-    <repeat name="rep_param_modifications_variable" min="0" max="1" title="param_modifications_variable">
+    <repeat name="rep_param_modifications_variable" min="0" title="param_modifications_variable">
       <param name="param_modifications_variable" type="select" optional="True" label="Variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable) e.g. 'Oxidation (M)'">
         <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
         <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
@@ -5263,26 +5284,31 @@
     <param name="param_modifications_variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help="(-variable_max_per_peptide) "/>
     <param name="param_peptide_missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help="(-missed_cleavages) "/>
     <param name="param_peptide_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
-      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Lys-N">Lys-N</option>
       <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="V8-DE">V8-DE</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
       <option value="Lys-C">Lys-C</option>
-      <option value="V8-E">V8-E</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
       <option value="no cleavage">no cleavage</option>
-      <option value="CNBr">CNBr</option>
+      <option value="Arg-C/P">Arg-C/P</option>
       <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="PepsinA">PepsinA</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="2-iodobenzoate">2-iodobenzoate</option>
       <option value="Arg-C">Arg-C</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="V8-E">V8-E</option>
+      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
+      <option value="Lys-C/P">Lys-C/P</option>
     </param>
     <param name="param_RNPxl_length" type="integer" value="2" label="Oligonucleotide maximum length" help="(-length) 0 = disable search for RNA variants"/>
     <param name="param_RNPxl_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
@@ -5362,5 +5388,5 @@
   <help>Annotate RNA to peptide crosslinks in MS/MS spectra.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/pub/OpenMS/develop-documentation/html/classRNPxlSearch.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlSearch.html</help>
 </tool>