--- a/SpectraMerger.xml	Wed Mar 01 12:42:48 2017 -0500
+++ b/SpectraMerger.xml	Wed Aug 09 09:35:00 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: [Signal processing and preprocessing]-->
-<tool id="SpectraMerger" name="SpectraMerger" version="2.1.0">
+<tool id="SpectraMerger" name="SpectraMerger" version="2.2.0">
   <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraMerger</token>
@@ -19,10 +19,20 @@
   -out $param_out
 #end if
 #if $param_merging_method:
-  -merging_method $param_merging_method
+  -merging_method
+  #if " " in str($param_merging_method):
+    "$param_merging_method"
+  #else
+    $param_merging_method
+  #end if
 #end if
 #if $param_algorithm_average_gaussian_spectrum_type:
-  -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type
+  -algorithm:average_gaussian:spectrum_type
+  #if " " in str($param_algorithm_average_gaussian_spectrum_type):
+    "$param_algorithm_average_gaussian_spectrum_type"
+  #else
+    $param_algorithm_average_gaussian_spectrum_type
+  #end if
 #end if
 #if $param_algorithm_average_gaussian_ms_level:
   -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
@@ -31,7 +41,12 @@
   -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
 #end if
 #if $param_algorithm_average_tophat_spectrum_type:
-  -algorithm:average_tophat:spectrum_type $param_algorithm_average_tophat_spectrum_type
+  -algorithm:average_tophat:spectrum_type
+  #if " " in str($param_algorithm_average_tophat_spectrum_type):
+    "$param_algorithm_average_tophat_spectrum_type"
+  #else
+    $param_algorithm_average_tophat_spectrum_type
+  #end if
 #end if
 #if $param_algorithm_average_tophat_ms_level:
   -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
@@ -40,7 +55,12 @@
   -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
 #end if
 #if $param_algorithm_average_tophat_rt_unit:
-  -algorithm:average_tophat:rt_unit $param_algorithm_average_tophat_rt_unit
+  -algorithm:average_tophat:rt_unit
+  #if " " in str($param_algorithm_average_tophat_rt_unit):
+    "$param_algorithm_average_tophat_rt_unit"
+  #else
+    $param_algorithm_average_tophat_rt_unit
+  #end if
 #end if
 
 #if $rep_param_algorithm_block_method_ms_levels:
@@ -73,10 +93,20 @@
   -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
 #end if
     #if $adv_opts.param_algorithm_mz_binning_width_unit:
-  -algorithm:mz_binning_width_unit $adv_opts.param_algorithm_mz_binning_width_unit
+  -algorithm:mz_binning_width_unit
+  #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
+    "$adv_opts.param_algorithm_mz_binning_width_unit"
+  #else
+    $adv_opts.param_algorithm_mz_binning_width_unit
+  #end if
 #end if
     #if $adv_opts.param_algorithm_sort_blocks:
-  -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks
+  -algorithm:sort_blocks
+  #if " " in str($adv_opts.param_algorithm_sort_blocks):
+    "$adv_opts.param_algorithm_sort_blocks"
+  #else
+    $adv_opts.param_algorithm_sort_blocks
+  #end if
 #end if
     #if $adv_opts.param_algorithm_average_gaussian_cutoff:
   -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff