--- a/MSSimulator.xml	Thu Apr 27 12:58:04 2017 -0400
+++ b/MSSimulator.xml	Fri Jul 14 18:56:04 2017 -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.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MSSimulator" name="MSSimulator" version="2.1.0">
+<tool id="MSSimulator" name="MSSimulator" version="2.2.0">
   <description>A highly configurable simulator for mass spectrometry experiments.</description>
   <macros>
     <token name="@EXECUTABLE@">MSSimulator</token>
@@ -352,6 +352,9 @@
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
 #end if
+#if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges:
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges
+#end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
 #end if
@@ -623,26 +626,26 @@
       </sanitizer>
     </param>
     <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) ">
-      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="Asp-N">Asp-N</option>
       <option value="Lys-C">Lys-C</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Formic_acid">Formic_acid</option>
-      <option value="Lys-C/P">Lys-C/P</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="V8-E">V8-E</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="PepsinA">PepsinA</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
     </param>
     <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
       <option value="trained">trained</option>
@@ -827,6 +830,7 @@
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/>
+    <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
     <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">