# HG changeset patch
# User galaxyp
# Date 1502286736 14400
# Node ID 190554cf21950313815d078b516fcf86b7c45030
# Parent  380ced982ec717e374b556882e9d305cd431fdee
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

diff -r 380ced982ec7 -r 190554cf2195 OpenSwathWorkflow.xml
--- a/OpenSwathWorkflow.xml	Wed Mar 01 12:53:40 2017 -0500
+++ b/OpenSwathWorkflow.xml	Wed Aug 09 09:52:16 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="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.1.0">
+<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0.1">
   <description>Complete workflow to run OpenSWATH</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
@@ -34,7 +34,10 @@
   -out_features $param_out_features
 #end if
 #if $param_out_tsv:
-  -out_tsv     "$param_out_tsv"
+  -out_tsv $param_out_tsv
+#end if
+#if $param_out_osw:
+  -out_osw $param_out_osw
 #end if
 #if $param_out_chrom:
   -out_chrom $param_out_chrom
@@ -48,6 +51,9 @@
 #if $param_ppm:
   -ppm
 #end if
+#if $param_sonar:
+  -sonar
+#end if
 #if $param_Scoring_stop_report_after_feature:
   -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
 #end if
@@ -67,10 +73,20 @@
   -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
 #end if
 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
-  -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction
+  -Scoring:TransitionGroupPicker:background_subtraction
+  #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction):
+    "$param_Scoring_TransitionGroupPicker_background_subtraction"
+  #else
+    $param_Scoring_TransitionGroupPicker_background_subtraction
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
-  -Scoring:TransitionGroupPicker:recalculate_peaks     "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
+  -Scoring:TransitionGroupPicker:recalculate_peaks
+  #if " " in str($param_Scoring_TransitionGroupPicker_recalculate_peaks):
+    "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
+  #else
+    $param_Scoring_TransitionGroupPicker_recalculate_peaks
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
   -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
@@ -79,7 +95,12 @@
   -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
 #end if
 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
-  -Scoring:TransitionGroupPicker:compute_peak_quality     "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
+  -Scoring:TransitionGroupPicker:compute_peak_quality
+  #if " " in str($param_Scoring_TransitionGroupPicker_compute_peak_quality):
+    "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
+  #else
+    $param_Scoring_TransitionGroupPicker_compute_peak_quality
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
   -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
@@ -103,10 +124,20 @@
   -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
 #end if
 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
-  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
+  #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks):
+    "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks"
+  #else
+    $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
-  -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
+    "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
+  #else
+    $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
+  #end if
 #end if
 #if $param_Scoring_DIAScoring_dia_extraction_window:
   -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
@@ -133,7 +164,12 @@
   -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
 #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
@@ -200,16 +236,37 @@
   -use_elution_model_score
 #end if
     #if $adv_opts.param_readOptions:
-  -readOptions $adv_opts.param_readOptions
+  -readOptions
+  #if " " in str($adv_opts.param_readOptions):
+    "$adv_opts.param_readOptions"
+  #else
+    $adv_opts.param_readOptions
+  #end if
 #end if
     #if $adv_opts.param_mz_correction_function:
-  -mz_correction_function $adv_opts.param_mz_correction_function
+  -mz_correction_function
+  #if " " in str($adv_opts.param_mz_correction_function):
+    "$adv_opts.param_mz_correction_function"
+  #else
+    $adv_opts.param_mz_correction_function
+  #end if
+#end if
+    #if $adv_opts.param_irt_mz_extraction_window:
+  -irt_mz_extraction_window $adv_opts.param_irt_mz_extraction_window
+#end if
+    #if $adv_opts.param_ppm_irtwindow:
+  -ppm_irtwindow
 #end if
     #if $adv_opts.param_tempDirectory:
   -tempDirectory     "$adv_opts.param_tempDirectory"
 #end if
     #if $adv_opts.param_extraction_function:
-  -extraction_function $adv_opts.param_extraction_function
+  -extraction_function
+  #if " " in str($adv_opts.param_extraction_function):
+    "$adv_opts.param_extraction_function"
+  #else
+    $adv_opts.param_extraction_function
+  #end if
 #end if
     #if $adv_opts.param_batchSize:
   -batchSize $adv_opts.param_batchSize
@@ -217,42 +274,107 @@
     #if $adv_opts.param_force:
   -force
 #end if
+    #if $adv_opts.param_Library_retentionTimeInterpretation:
+  -Library:retentionTimeInterpretation
+  #if " " in str($adv_opts.param_Library_retentionTimeInterpretation):
+    "$adv_opts.param_Library_retentionTimeInterpretation"
+  #else
+    $adv_opts.param_Library_retentionTimeInterpretation
+  #end if
+#end if
+    #if $adv_opts.param_Library_override_group_label_check:
+  -Library:override_group_label_check
+#end if
+    #if $adv_opts.param_Library_force_invalid_mods:
+  -Library:force_invalid_mods
+#end if
     #if $adv_opts.param_Scoring_quantification_cutoff:
   -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
 #end if
     #if $adv_opts.param_Scoring_write_convex_hull:
   -Scoring:write_convex_hull
 #end if
+    #if $adv_opts.param_Scoring_TransitionGroupPicker_use_precursors:
+  -Scoring:TransitionGroupPicker:use_precursors
+#end if
     #if $adv_opts.param_Scoring_Scores_use_shape_score:
-  -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score
+  -Scoring:Scores:use_shape_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
+    "$adv_opts.param_Scoring_Scores_use_shape_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_shape_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_coelution_score:
-  -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score
+  -Scoring:Scores:use_coelution_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score):
+    "$adv_opts.param_Scoring_Scores_use_coelution_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_coelution_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_rt_score:
-  -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score
+  -Scoring:Scores:use_rt_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score):
+    "$adv_opts.param_Scoring_Scores_use_rt_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_rt_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_library_score:
-  -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score
+  -Scoring:Scores:use_library_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_library_score):
+    "$adv_opts.param_Scoring_Scores_use_library_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_library_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_intensity_score:
-  -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score
+  -Scoring:Scores:use_intensity_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score):
+    "$adv_opts.param_Scoring_Scores_use_intensity_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_intensity_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
-  -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score
+  -Scoring:Scores:use_nr_peaks_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score):
+    "$adv_opts.param_Scoring_Scores_use_nr_peaks_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_nr_peaks_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
-  -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score
+  -Scoring:Scores:use_total_xic_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score):
+    "$adv_opts.param_Scoring_Scores_use_total_xic_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_total_xic_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_sn_score:
-  -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score
+  -Scoring:Scores:use_sn_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score):
+    "$adv_opts.param_Scoring_Scores_use_sn_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_sn_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_dia_scores:
-  -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores
+  -Scoring:Scores:use_dia_scores
+  #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores):
+    "$adv_opts.param_Scoring_Scores_use_dia_scores"
+  #else
+    $adv_opts.param_Scoring_Scores_use_dia_scores
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
   -Scoring:Scores:use_ms1_correlation
 #end if
+    #if $adv_opts.param_Scoring_Scores_use_sonar_scores:
+  -Scoring:Scores:use_sonar_scores
+#end if
     #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
   -Scoring:Scores:use_ms1_fullscan
 #end if
@@ -262,7 +384,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
+    <param name="param_in" type="data" format="mzml,mzxml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -270,24 +392,17 @@
         </valid>
       </sanitizer>
     </param>
-    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/>
+    <param name="param_tr" type="data" format="traml,tabular,pqp" optional="False" label="transition file ('TraML','tsv','pqp')" help="(-tr) "/>
     <param name="param_tr_type" display="radio" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) ">
       <option value="traML">traML</option>
       <option value="tsv">tsv</option>
-      <option value="csv">csv</option>
+      <option value="pqp">pqp</option>
     </param>
     <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
-    <param name="param_out_tsv" type="text" size="30" label="TSV output file (mProphet compatible)" help="(-out_tsv) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
     <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/>
     <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/>
     <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
+    <param name="param_sonar" display="radio" type="boolean" truevalue="-sonar" falsevalue="" checked="false" optional="True" label="data is scanning SWATH data" help="(-sonar) "/>
     <param name="param_Scoring_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/>
     <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/>
     <param name="param_Scoring_uis_threshold_sn" type="integer" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help="(-uis_threshold_sn) "/>
@@ -299,23 +414,15 @@
       <option value="smoothed">smoothed</option>
       <option value="original">original</option>
     </param>
-    <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="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">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" display="radio" type="select" optional="False" value="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">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
     </param>
     <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" 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_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
-    <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="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">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" display="radio" type="select" optional="False" value="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">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
     </param>
     <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/>
     <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
@@ -359,7 +466,7 @@
     <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
     <expand macro="advanced_options">
       <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/>
-      <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
+      <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
       <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
       <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
       <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/>
@@ -373,6 +480,7 @@
         <option value="normal" selected="true">normal</option>
         <option value="cache">cache</option>
         <option value="cacheWorkingInMemory">cacheWorkingInMemory</option>
+        <option value="workingInMemory">workingInMemory</option>
       </param>
       <param name="param_mz_correction_function" type="select" optional="False" value="none" label="Use the retention time normalization peptide MS2 masses to perform a mass correction (linear, weighted by intensity linear or quadratic) of all spectra" help="(-mz_correction_function) ">
         <option value="none" selected="true">none</option>
@@ -383,6 +491,8 @@
         <option value="weighted_quadratic_regression_delta_ppm">weighted_quadratic_regression_delta_ppm</option>
         <option value="quadratic_regression_delta_ppm">quadratic_regression_delta_ppm</option>
       </param>
+      <param name="param_irt_mz_extraction_window" type="float" value="0.05" label="Extraction window used for iRT and m/z correction (in Thomson, use ppm use -ppm flag)" help="(-irt_mz_extraction_window) "/>
+      <param name="param_ppm_irtwindow" display="radio" type="boolean" truevalue="-ppm_irtwindow" falsevalue="" checked="false" optional="True" label="iRT m/z extraction_window is in ppm" help="(-ppm_irtwindow) "/>
       <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
         <sanitizer>
           <valid initial="string.printable">
@@ -397,8 +507,16 @@
       </param>
       <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/>
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_Library_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
+        <option value="iRT" selected="true">iRT</option>
+        <option value="seconds">seconds</option>
+        <option value="minutes">minutes</option>
+      </param>
+      <param name="param_Library_override_group_label_check" display="radio" type="boolean" truevalue="-Library:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
+      <param name="param_Library_force_invalid_mods" display="radio" type="boolean" truevalue="-Library:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
       <param name="param_Scoring_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>
       <param name="param_Scoring_write_convex_hull" display="radio" type="boolean" truevalue="-Scoring:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>
+      <param name="param_Scoring_TransitionGroupPicker_use_precursors" display="radio" type="boolean" truevalue="-Scoring:TransitionGroupPicker:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
       <param name="param_Scoring_Scores_use_shape_score" display="radio" type="select" optional="False" value="true" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) ">
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
@@ -431,17 +549,20 @@
         <option value="true" selected="true">true</option>
         <option value="false">false</option>
       </param>
-      <param name="param_Scoring_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_Scoring_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_Scoring_Scores_use_ms1_correlation" display="radio" type="boolean" truevalue="-Scoring: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_Scoring_Scores_use_sonar_scores" display="radio" type="boolean" truevalue="-Scoring: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_Scoring_Scores_use_ms1_fullscan" display="radio" type="boolean" truevalue="-Scoring: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_Scoring_Scores_use_uis_scores" display="radio" type="boolean" truevalue="-Scoring:Scores:use_uis_scores" falsevalue="" checked="false" optional="True" label="Use UIS scores for peptidoform identification" help="(-use_uis_scores) "/>
     </expand>
   </inputs>
   <outputs>
     <data name="param_out_features" format="featurexml"/>
+    <data name="param_out_tsv" format="tabular"/>
+    <data name="param_out_osw" format="osw"/>
     <data name="param_out_chrom" format="mzml"/>
   </outputs>
   <help>Complete workflow to run OpenSWATH
diff -r 380ced982ec7 -r 190554cf2195 datatypes_conf.xml
--- a/datatypes_conf.xml	Wed Mar 01 12:53:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<datatypes>
-  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
-    <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/>
-    <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/>
-    <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/>
-    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/>
-    <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/>
-    <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/>
-    <datatype extension="grid" type="galaxy.datatypes.data:Grid"/>
-    <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/>
-    <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/>
-    <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/>
-    <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/>
-    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-    <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/>
-    <datatype extension="txt" type="galaxy.datatypes.data:Text"/>
-  </registration>
-</datatypes>
diff -r 380ced982ec7 -r 190554cf2195 filetypes.txt
--- a/filetypes.txt	Wed Mar 01 12:53:40 2017 -0500
+++ b/filetypes.txt	Wed Aug 09 09:52:16 2017 -0400
@@ -14,7 +14,7 @@
 consensusXML  consensusxml      galaxy.datatypes.proteomics:ConsensusXML    application/xml
 edta          tabular           galaxy.datatypes.tabular:Tabular 
 featureXML    featurexml        galaxy.datatypes.proteomics:FeatureXML      application/xml
-idXML         idxml             galaxy.datatypes.proteomics:IdXM            application/xml
+idXML         idxml             galaxy.datatypes.proteomics:IdXML           application/xml
 mzML          mzml              galaxy.datatypes.proteomics:MzML            application/xml
 mzXML         mzxml             galaxy.datatypes.proteomics:MzXML           application/xml
 pepXML        pepxml            galaxy.datatypes.proteomics:PepXml          application/xml
@@ -26,4 +26,4 @@
 msp           msp               galaxy.datatypes.proteomics:Msp
 mzid          mzid              galaxy.datatypes.proteomics:MzIdentML       application/xml
 png           png               galaxy.datatypes.images:Png                 image/png
-mgf           mgf               galaxy.datatypes.proteomics:Mgf
\ No newline at end of file
+mgf           mgf               galaxy.datatypes.proteomics:Mgf
diff -r 380ced982ec7 -r 190554cf2195 macros.xml
--- a/macros.xml	Wed Mar 01 12:53:40 2017 -0500
+++ b/macros.xml	Wed Aug 09 09:52:16 2017 -0400
@@ -2,7 +2,7 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.1">openms</requirement>
+      <requirement type="package" version="2.2">openms</requirement>
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
diff -r 380ced982ec7 -r 190554cf2195 readme.md
--- a/readme.md	Wed Mar 01 12:53:40 2017 -0500
+++ b/readme.md	Wed Aug 09 09:52:16 2017 -0400
@@ -14,15 +14,29 @@
 Generating OpenMS wrappers
 ==========================
 
- * install OpenMS (you can do this automatically through the Tool Shed)
+ * install OpenMS (you can do this automatically through Conda)
  * create a folder called CTD
- * inside of your new installed openms/bin folder, execute the following command:
+ * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory:
     
     ```bash
     for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
     ```
     
- * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
+ * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow:
+ 
+    ```bash
+    ls >> tools.txt
+    ```
+    
+ * search for the `bin` folder of your conda environment containing OpenMS and do:
+ 
+    ```bash
+    while read p; do
+        ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD;
+    done <tools.txt
+    ```
+    
+ * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`).
 
  * clone or install CTDopts
 
@@ -39,10 +53,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. 
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it.
 
     ```bash
     python generator.py \ 
@@ -102,17 +116,32 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
+    
+ * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
+   ```
+    <command><![CDATA[
    
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+      ## check input file type
+      #set $in_type = $param_in.ext
+
+      ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
+      ln -s '$param_in' 'param_in.${in_type}' &&
+
+      IDFileConverter
 
- * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
+      #if $param_in:
+        -in 'param_in.${in_type}'
+      #end if
+
+        [...]
+        ]]>
+    ```
+
+ * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.:
  
-        <data name="param_out" metadata_source="param_in" auto_format="true"/>
+   - `<data name="param_out" auto_format="true"/>`
+   - `<data name="param_out" metadata_source="param_in" auto_format="true"/>`
         
  * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files.
  
diff -r 380ced982ec7 -r 190554cf2195 tool.conf
--- a/tool.conf	Wed Mar 01 12:53:40 2017 -0500
+++ b/tool.conf	Wed Aug 09 09:52:16 2017 -0400
@@ -6,13 +6,7 @@
     <tool file="openms/RTModel.xml"/>
     <tool file="openms/RTPredict.xml"/>
   </section>
-  <section id="section-id-DEFAULT" name="DEFAULT">
-    <tool file="openms/OpenSwathFileSplitter.xml"/>
-    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
-  </section>
   <section id="section-id-TargetedExperiments" name="Targeted Experiments">
-    <tool file="openms/ConvertTraMLToTSV.xml"/>
-    <tool file="openms/ConvertTSVToTraML.xml"/>
     <tool file="openms/InclusionExclusionListCreator.xml"/>
     <tool file="openms/MRMMapper.xml"/>
     <tool file="openms/OpenSwathAnalyzer.xml"/>
@@ -22,13 +16,17 @@
     <tool file="openms/OpenSwathDecoyGenerator.xml"/>
     <tool file="openms/OpenSwathDIAPreScoring.xml"/>
     <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/>
+    <tool file="openms/OpenSwathFileSplitter.xml"/>
+    <tool file="openms/OpenSwathMzMLFileCacher.xml"/>
     <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/>
     <tool file="openms/OpenSwathRTNormalizer.xml"/>
     <tool file="openms/PrecursorIonSelector.xml"/>
+    <tool file="openms/TargetedFileConverter.xml"/>
   </section>
   <section id="section-id-Utilities" name="Utilities">
     <tool file="openms/AccurateMassSearch.xml"/>
     <tool file="openms/CVInspector.xml"/>
+    <tool file="openms/DatabaseFilter.xml"/>
     <tool file="openms/DecoyDatabase.xml"/>
     <tool file="openms/DeMeanderize.xml"/>
     <tool file="openms/Digestor.xml"/>
@@ -44,7 +42,6 @@
     <tool file="openms/LabeledEval.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes.xml"/>
     <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/>
-    <tool file="openms/MapAlignmentEvaluation.xml"/>
     <tool file="openms/MassCalculator.xml"/>
     <tool file="openms/MetaboliteSpectralMatcher.xml"/>
     <tool file="openms/MetaProSIP.xml"/>
@@ -62,12 +59,14 @@
     <tool file="openms/QCMerger.xml"/>
     <tool file="openms/QCShrinker.xml"/>
     <tool file="openms/RNPxl.xml"/>
+    <tool file="openms/RNPxlSearch.xml"/>
     <tool file="openms/RNPxlXICFilter.xml"/>
     <tool file="openms/RTEvaluation.xml"/>
     <tool file="openms/SemanticValidator.xml"/>
     <tool file="openms/SequenceCoverageCalculator.xml"/>
     <tool file="openms/SimpleSearchEngine.xml"/>
     <tool file="openms/SpecLibCreator.xml"/>
+    <tool file="openms/SpectraSTSearchAdapter.xml"/>
     <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/>
     <tool file="openms/TICCalculator.xml"/>
     <tool file="openms/TopPerc.xml"/>
@@ -78,6 +77,7 @@
     <tool file="openms/ConsensusMapNormalizer.xml"/>
     <tool file="openms/FeatureLinkerLabeled.xml"/>
     <tool file="openms/FeatureLinkerUnlabeled.xml"/>
+    <tool file="openms/FeatureLinkerUnlabeledKD.xml"/>
     <tool file="openms/FeatureLinkerUnlabeledQT.xml"/>
     <tool file="openms/MapRTTransformer.xml"/>
   </section>
@@ -154,9 +154,7 @@
     <tool file="openms/FeatureFinderMultiplex.xml"/>
     <tool file="openms/FeatureFinderSuperHirn.xml"/>
     <tool file="openms/IsobaricAnalyzer.xml"/>
-    <tool file="openms/ITRAQAnalyzer.xml"/>
     <tool file="openms/ProteinQuantifier.xml"/>
     <tool file="openms/ProteinResolver.xml"/>
-    <tool file="openms/TMTAnalyzer.xml"/>
   </section>
 </toolbox>