--- a/MSSimulator.xml	Wed Mar 01 12:59:29 2017 -0500
+++ b/MSSimulator.xml	Wed Aug 09 09:59:36 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>
@@ -38,10 +38,20 @@
   -out_id $param_out_id
 #end if
 #if $param_algorithm_MSSim_Digestion_enzyme:
-  -algorithm:MSSim:Digestion:enzyme $param_algorithm_MSSim_Digestion_enzyme
+  -algorithm:MSSim:Digestion:enzyme
+  #if " " in str($param_algorithm_MSSim_Digestion_enzyme):
+    "$param_algorithm_MSSim_Digestion_enzyme"
+  #else
+    $param_algorithm_MSSim_Digestion_enzyme
+  #end if
 #end if
 #if $param_algorithm_MSSim_Digestion_model:
-  -algorithm:MSSim:Digestion:model $param_algorithm_MSSim_Digestion_model
+  -algorithm:MSSim:Digestion:model
+  #if " " in str($param_algorithm_MSSim_Digestion_model):
+    "$param_algorithm_MSSim_Digestion_model"
+  #else
+    $param_algorithm_MSSim_Digestion_model
+  #end if
 #end if
 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
   -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
@@ -53,10 +63,20 @@
   -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
 #end if
 #if $param_algorithm_MSSim_RT_rt_column:
-  -algorithm:MSSim:RT:rt_column $param_algorithm_MSSim_RT_rt_column
+  -algorithm:MSSim:RT:rt_column
+  #if " " in str($param_algorithm_MSSim_RT_rt_column):
+    "$param_algorithm_MSSim_RT_rt_column"
+  #else
+    $param_algorithm_MSSim_RT_rt_column
+  #end if
 #end if
 #if $param_algorithm_MSSim_RT_auto_scale:
-  -algorithm:MSSim:RT:auto_scale $param_algorithm_MSSim_RT_auto_scale
+  -algorithm:MSSim:RT:auto_scale
+  #if " " in str($param_algorithm_MSSim_RT_auto_scale):
+    "$param_algorithm_MSSim_RT_auto_scale"
+  #else
+    $param_algorithm_MSSim_RT_auto_scale
+  #end if
 #end if
 #if $param_algorithm_MSSim_RT_total_gradient_time:
   -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
@@ -167,16 +187,31 @@
   -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
 #end if
 #if $param_algorithm_MSSim_RawSignal_enabled:
-  -algorithm:MSSim:RawSignal:enabled $param_algorithm_MSSim_RawSignal_enabled
+  -algorithm:MSSim:RawSignal:enabled
+  #if " " in str($param_algorithm_MSSim_RawSignal_enabled):
+    "$param_algorithm_MSSim_RawSignal_enabled"
+  #else
+    $param_algorithm_MSSim_RawSignal_enabled
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_peak_shape:
-  -algorithm:MSSim:RawSignal:peak_shape $param_algorithm_MSSim_RawSignal_peak_shape
+  -algorithm:MSSim:RawSignal:peak_shape
+  #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape):
+    "$param_algorithm_MSSim_RawSignal_peak_shape"
+  #else
+    $param_algorithm_MSSim_RawSignal_peak_shape
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_resolution_value:
   -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
 #end if
 #if $param_algorithm_MSSim_RawSignal_resolution_type:
-  -algorithm:MSSim:RawSignal:resolution:type $param_algorithm_MSSim_RawSignal_resolution_type
+  -algorithm:MSSim:RawSignal:resolution:type
+  #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type):
+    "$param_algorithm_MSSim_RawSignal_resolution_type"
+  #else
+    $param_algorithm_MSSim_RawSignal_resolution_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
   -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
@@ -221,7 +256,12 @@
   -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_status:
-  -algorithm:MSSim:RawTandemSignal:status $param_algorithm_MSSim_RawTandemSignal_status
+  -algorithm:MSSim:RawTandemSignal:status
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_status):
+    "$param_algorithm_MSSim_RawTandemSignal_status"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_status
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
   -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
@@ -312,6 +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
@@ -319,10 +362,20 @@
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
-  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions):
+    "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
-  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
+  -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
+  #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions):
+    "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions"
+  #else
+    $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
+  #end if
 #end if
 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
   -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
@@ -427,16 +480,31 @@
   -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
 #end if
 #if $param_algorithm_MSSim_Global_ionization_type:
-  -algorithm:MSSim:Global:ionization_type $param_algorithm_MSSim_Global_ionization_type
+  -algorithm:MSSim:Global:ionization_type
+  #if " " in str($param_algorithm_MSSim_Global_ionization_type):
+    "$param_algorithm_MSSim_Global_ionization_type"
+  #else
+    $param_algorithm_MSSim_Global_ionization_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_type:
-  -algorithm:MSSim:Labeling:type $param_algorithm_MSSim_Labeling_type
+  -algorithm:MSSim:Labeling:type
+  #if " " in str($param_algorithm_MSSim_Labeling_type):
+    "$param_algorithm_MSSim_Labeling_type"
+  #else
+    $param_algorithm_MSSim_Labeling_type
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
   -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
 #end if
 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
-  -algorithm:MSSim:Labeling:ICPL:label_proteins $param_algorithm_MSSim_Labeling_ICPL_label_proteins
+  -algorithm:MSSim:Labeling:ICPL:label_proteins
+  #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins):
+    "$param_algorithm_MSSim_Labeling_ICPL_label_proteins"
+  #else
+    $param_algorithm_MSSim_Labeling_ICPL_label_proteins
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
   -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
@@ -454,7 +522,12 @@
   -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine     "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
 #end if
 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
-  -algorithm:MSSim:Labeling:itraq:iTRAQ $param_algorithm_MSSim_Labeling_itraq_iTRAQ
+  -algorithm:MSSim:Labeling:itraq:iTRAQ
+  #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
+    "$param_algorithm_MSSim_Labeling_itraq_iTRAQ"
+  #else
+    $param_algorithm_MSSim_Labeling_itraq_iTRAQ
+  #end if
 #end if
 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
   -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
@@ -488,10 +561,20 @@
   -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
 #end if
 #if $param_algorithm_RandomNumberGenerators_biological:
-  -algorithm:RandomNumberGenerators:biological $param_algorithm_RandomNumberGenerators_biological
+  -algorithm:RandomNumberGenerators:biological
+  #if " " in str($param_algorithm_RandomNumberGenerators_biological):
+    "$param_algorithm_RandomNumberGenerators_biological"
+  #else
+    $param_algorithm_RandomNumberGenerators_biological
+  #end if
 #end if
 #if $param_algorithm_RandomNumberGenerators_technical:
-  -algorithm:RandomNumberGenerators:technical $param_algorithm_RandomNumberGenerators_technical
+  -algorithm:RandomNumberGenerators:technical
+  #if " " in str($param_algorithm_RandomNumberGenerators_technical):
+    "$param_algorithm_RandomNumberGenerators_technical"
+  #else
+    $param_algorithm_RandomNumberGenerators_technical
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -543,26 +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>
@@ -747,6 +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) ">