--- a/OpenSwathRTNormalizer.xml	Wed Mar 01 12:16:05 2017 -0500
+++ b/OpenSwathRTNormalizer.xml	Wed Aug 09 08:58:14 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: [Targeted Experiments]-->
-<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.1.0">
+<tool id="OpenSwathRTNormalizer" name="OpenSwathRTNormalizer" version="2.2.0">
   <description>This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathRTNormalizer</token>
@@ -65,7 +65,12 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
@@ -80,13 +85,23 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  #end if
 #end if
 #if $param_algorithm_DIAScoring_dia_extraction_window:
   -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
@@ -110,7 +125,12 @@
   -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
 #end if
 #if $param_outlierDetection_outlierMethod:
-  -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
+  -outlierDetection:outlierMethod
+  #if " " in str($param_outlierDetection_outlierMethod):
+    "$param_outlierDetection_outlierMethod"
+  #else
+    $param_outlierDetection_outlierMethod
+  #end if
 #end if
 #if $param_outlierDetection_useIterativeChauvenet:
   -outlierDetection:useIterativeChauvenet
@@ -159,10 +179,18 @@
   -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
-  -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  -algorithm:TransitionGroupPicker:background_subtraction
+  #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
+    "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
+  #else
+    $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  #end if
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
-  -algorithm:TransitionGroupPicker:recalculate_peaks     "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
+  -algorithm:TransitionGroupPicker:recalculate_peaks
+#end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_use_precursors:
+  -algorithm:TransitionGroupPicker:use_precursors
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
   -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
@@ -171,7 +199,7 @@
   -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
-  -algorithm:TransitionGroupPicker:compute_peak_quality     "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
+  -algorithm:TransitionGroupPicker:compute_peak_quality
 #end if
     #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
   -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
@@ -189,38 +217,91 @@
   -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
 #end if
     #if $adv_opts.param_algorithm_Scores_use_shape_score:
-  -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
+  -algorithm:Scores:use_shape_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
+    "$adv_opts.param_algorithm_Scores_use_shape_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_shape_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_coelution_score:
-  -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
+  -algorithm:Scores:use_coelution_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
+    "$adv_opts.param_algorithm_Scores_use_coelution_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_coelution_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_rt_score:
-  -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
+  -algorithm:Scores:use_rt_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
+    "$adv_opts.param_algorithm_Scores_use_rt_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_rt_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_library_score:
-  -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
+  -algorithm:Scores:use_library_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
+    "$adv_opts.param_algorithm_Scores_use_library_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_library_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
-  -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
+  -algorithm:Scores:use_elution_model_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
+    "$adv_opts.param_algorithm_Scores_use_elution_model_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_elution_model_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_intensity_score:
-  -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
+  -algorithm:Scores:use_intensity_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
+    "$adv_opts.param_algorithm_Scores_use_intensity_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_intensity_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
-  -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  -algorithm:Scores:use_nr_peaks_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
+    "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
-  -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
+  -algorithm:Scores:use_total_xic_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
+    "$adv_opts.param_algorithm_Scores_use_total_xic_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_total_xic_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_sn_score:
-  -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
+  -algorithm:Scores:use_sn_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
+    "$adv_opts.param_algorithm_Scores_use_sn_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_sn_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_dia_scores:
-  -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
+  -algorithm:Scores:use_dia_scores
+  #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
+    "$adv_opts.param_algorithm_Scores_use_dia_scores"
+  #else
+    $adv_opts.param_algorithm_Scores_use_dia_scores
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
   -algorithm:Scores:use_ms1_correlation
 #end if
+    #if $adv_opts.param_algorithm_Scores_use_sonar_scores:
+  -algorithm:Scores:use_sonar_scores
+#end if
     #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
   -algorithm:Scores:use_ms1_fullscan
 #end if
@@ -305,24 +386,11 @@
         <option value="smoothed">smoothed</option>
         <option value="original">original</option>
       </param>
-      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
+      <param name="param_algorithm_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
       <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
       <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
-      <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
       <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
       <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
       <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
@@ -364,11 +432,12 @@
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
       </param>
-      <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) ">
+      <param name="param_algorithm_Scores_use_dia_scores" display="radio" type="select" optional="False" value="true" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) If turned off, will not use fragment ion spectra for scoring">
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
       </param>
       <param name="param_algorithm_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
+      <param name="param_algorithm_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_sonar_scores" falsevalue="" checked="false" optional="True" label="Use the scores for SONAR scans (scanning swath)" help="(-use_sonar_scores) "/>
       <param name="param_algorithm_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
       <param name="param_algorithm_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-algorithm:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
     </expand>