--- a/OpenSwathAnalyzer.xml	Mon Feb 12 08:56:21 2018 -0500
+++ b/OpenSwathAnalyzer.xml	Wed May 15 06:46:18 2019 -0400
@@ -1,8 +1,8 @@
 <?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: [Targeted Experiments]-->
-<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.2.0">
-  <description>Picks peaks and finds features in an SRM experiment.</description>
+<tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.3.0">
+  <description>Picks peaks and finds features in an SWATH-MS or SRM experiment.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathAnalyzer</token>
     <import>macros.xml</import>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>OpenSwathAnalyzer
+  <command detect_errors="aggressive"><![CDATA[OpenSwathAnalyzer
 
 #if $param_in:
   -in $param_in
@@ -174,6 +174,9 @@
     #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
   -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
 #end if
+    #if $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary:
+  -algorithm:TransitionGroupPicker:resample_boundary $adv_opts.param_algorithm_TransitionGroupPicker_resample_boundary
+#end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
   -algorithm:TransitionGroupPicker:compute_peak_quality
 #end if
@@ -285,7 +288,7 @@
   -algorithm:Scores:use_uis_scores
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/>
     <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
@@ -314,7 +317,7 @@
       <option value="false">false</option>
       <option value="true" selected="true">true</option>
     </param>
-    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
     <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
     <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
     <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
@@ -323,9 +326,9 @@
       <option value="false">false</option>
     </param>
     <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
-    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
-      <option value="legacy" selected="true">legacy</option>
-      <option value="corrected">corrected</option>
+    <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" display="radio" type="select" optional="False" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed chromatogram or Crawdad on smoothed chromatogram)" help="(-method) ">
+      <option value="legacy">legacy</option>
+      <option value="corrected" selected="true">corrected</option>
       <option value="crawdad">crawdad</option>
     </param>
     <param name="param_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
@@ -358,6 +361,7 @@
       <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_resample_boundary" type="float" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help="(-resample_boundary) "/>
       <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) "/>
@@ -413,8 +417,8 @@
   <outputs>
     <data name="param_out" format="featurexml"/>
   </outputs>
-  <help>Picks peaks and finds features in an SRM experiment.
+  <help>Picks peaks and finds features in an SWATH-MS or SRM experiment.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_OpenSwathAnalyzer.html</help>
 </tool>