--- a/OpenSwathWorkflow.xml	Thu Sep 24 12:05:36 2020 +0000
+++ b/OpenSwathWorkflow.xml	Tue Oct 13 20:19:13 2020 +0000
@@ -28,6 +28,10 @@
   mkdir tr_irt_nonlinear &&
   ln -s '$tr_irt_nonlinear' 'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)' &&
 #end if
+#if $swath_windows_file:
+  mkdir swath_windows_file &&
+  ln -s '$swath_windows_file' 'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)' &&
+#end if
 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_features &&
 #end if
@@ -54,10 +58,6 @@
     mkdir adv_opts_cond.rt_norm &&
     ln -s '$adv_opts_cond.rt_norm' 'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)' &&
   #end if
-  #if $adv_opts_cond.swath_windows_file:
-    mkdir adv_opts_cond.swath_windows_file &&
-    ln -s '$adv_opts_cond.swath_windows_file' 'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)' &&
-  #end if
 #end if
 
 ## Main program call
@@ -78,6 +78,10 @@
   -tr_irt_nonlinear
   'tr_irt_nonlinear/${re.sub("[^\w\-_]", "_", $tr_irt_nonlinear.element_identifier)}.$gxy2omsext($tr_irt_nonlinear.ext)'
 #end if
+#if $swath_windows_file:
+  -swath_windows_file
+  'swath_windows_file/${re.sub("[^\w\-_]", "_", $swath_windows_file.element_identifier)}.$gxy2omsext($swath_windows_file.ext)'
+#end if
 #if "out_features_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_features
   'out_features/output.${gxy2omsext("featurexml")}'
@@ -111,10 +115,6 @@
     -rt_norm
     'adv_opts_cond.rt_norm/${re.sub("[^\w\-_]", "_", $adv_opts_cond.rt_norm.element_identifier)}.$gxy2omsext($adv_opts_cond.rt_norm.ext)'
   #end if
-  #if $adv_opts_cond.swath_windows_file:
-    -swath_windows_file
-    'adv_opts_cond.swath_windows_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.swath_windows_file.element_identifier)}.$gxy2omsext($adv_opts_cond.swath_windows_file.ext)'
-  #end if
 #end if
 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
   | tee '$stdout'
@@ -154,11 +154,12 @@
     <param name="tr" argument="-tr" type="data" format="pqp,tabular,traml" optional="false" label="transition file ('TraML','tsv','pqp')" help=" select pqp,tabular,traml data sets(s)"/>
     <param name="tr_irt" argument="-tr_irt" type="data" format="pqp,tabular,traml" optional="true" label="transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
     <param name="tr_irt_nonlinear" argument="-tr_irt_nonlinear" type="data" format="pqp,tabular,traml" optional="true" label="additional nonlinear transition file ('TraML')" help=" select pqp,tabular,traml data sets(s)"/>
+    <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
     <param name="sonar" argument="-sonar" type="boolean" truevalue="true" falsevalue="false" checked="false" label="data is scanning SWATH data" help=""/>
     <param name="rt_extraction_window" argument="-rt_extraction_window" type="float" optional="true" 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=""/>
     <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
-    <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
-    <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
+    <param name="mz_extraction_window" argument="-mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window in Thomson or ppm (see mz_extraction_window_unit)" help=""/>
+    <param name="mz_extraction_window_ms1" argument="-mz_extraction_window_ms1" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used in MS1 in Thomson or ppm (see mz_extraction_window_ms1_unit)" help=""/>
     <param name="im_extraction_window_ms1" argument="-im_extraction_window_ms1" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension for MS1 (in milliseconds)" help=""/>
     <section name="Calibration" title="Parameters for the m/z and ion mobility calibration" help="" expanded="false">
       <param name="ms1_im_calibration" argument="-Calibration:ms1_im_calibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to use MS1 precursor data for the ion mobility calibration (default = false, uses MS2 / fragment ions for calibration)" help=""/>
@@ -210,7 +211,7 @@
       <param name="MinPeptidesPerBin" argument="-RTNormalization:MinPeptidesPerBin" type="integer" optional="true" value="1" label="Minimal number of peptides that are required for a bin to counted as 'covered'" help=""/>
       <param name="MinBinsFilled" argument="-RTNormalization:MinBinsFilled" type="integer" optional="true" value="8" label="Minimal number of bins required to be covered" help=""/>
       <section name="lowess" title="" help="" expanded="false">
-        <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.666666666666667" label="Span parameter for lowess" help=""/>
+        <param name="span" argument="-RTNormalization:lowess:span" type="float" optional="true" min="0.0" max="1.0" value="0.05" label="Span parameter for lowess" help=""/>
       </section>
       <section name="b_spline" title="" help="" expanded="false">
         <param name="num_nodes" argument="-RTNormalization:b_spline:num_nodes" type="integer" optional="true" min="0" value="5" label="Number of nodes for b spline" help=""/>
@@ -228,7 +229,7 @@
       </param>
       <param name="add_up_spectra" argument="-Scoring:add_up_spectra" type="integer" optional="true" min="1" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help=""/>
       <param name="spacing_for_spectra_resampling" argument="-Scoring:spacing_for_spectra_resampling" type="float" optional="true" min="0.0" value="0.005" label="If spectra are to be added, use this spacing to add them up" help=""/>
-      <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="0" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
+      <param name="uis_threshold_sn" argument="-Scoring:uis_threshold_sn" type="integer" optional="true" value="-1" label="S/N threshold to consider identification transition (set to -1 to consider all)" help=""/>
       <param name="uis_threshold_peak_area" argument="-Scoring:uis_threshold_peak_area" type="integer" optional="true" value="0" label="Peak area threshold to consider identification transition (set to -1 to consider all)" help=""/>
       <param name="scoring_model" argument="-Scoring:scoring_model" display="radio" type="select" optional="false" label="Scoring model to use" help="">
         <option value="default" selected="true">default</option>
@@ -236,6 +237,9 @@
         <expand macro="list_string_san"/>
       </param>
       <param name="im_extra_drift" argument="-Scoring:im_extra_drift" type="float" optional="true" min="0.0" value="0.0" label="Extra drift time to extract for IM scoring (as a fraction" help="e.g. 0.25 means 25% extra on each side)"/>
+      <param name="strict" argument="-Scoring:strict" type="text" optional="true" value="true" label="Whether to error (true) or skip (false) if a transition in a transition group does not have a corresponding chromatogram" help="">
+        <expand macro="list_string_san"/>
+      </param>
       <section name="TransitionGroupPicker" title="" help="" expanded="false">
         <param name="stop_after_feature" argument="-Scoring:TransitionGroupPicker:stop_after_feature" type="integer" optional="true" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help=""/>
         <param name="min_peak_width" argument="-Scoring:TransitionGroupPicker:min_peak_width" type="float" optional="true" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help=""/>
@@ -256,7 +260,7 @@
         <param name="recalculate_peaks_max_z" argument="-Scoring:TransitionGroupPicker:recalculate_peaks_max_z" type="float" optional="true" value="0.75" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
         <param name="minimal_quality" argument="-Scoring:TransitionGroupPicker:minimal_quality" type="float" optional="true" value="-1.5" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help=""/>
         <param name="resample_boundary" argument="-Scoring:TransitionGroupPicker:resample_boundary" type="float" optional="true" value="15.0" label="For computing peak quality, how many extra seconds should be sample left and right of the actual peak" help=""/>
-        <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
+        <param name="compute_peak_quality" argument="-Scoring:TransitionGroupPicker:compute_peak_quality" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
         <param name="compute_peak_shape_metrics" argument="-Scoring:TransitionGroupPicker:compute_peak_shape_metrics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculates various peak shape metrics" help="(e.g., tailing) that can be used for downstream QC/QA"/>
         <param name="compute_total_mi" argument="-Scoring:TransitionGroupPicker:compute_total_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute mutual information metrics for individual transitions that can be used for OpenSWATH/IPF scoring" help=""/>
         <param name="boundary_selection_method" argument="-Scoring:TransitionGroupPicker:boundary_selection_method" display="radio" type="select" optional="false" label="Method to use when selecting the best boundaries for peaks" help="">
@@ -324,22 +328,21 @@
         <param name="use_total_xic_score" argument="-Scoring:Scores:use_total_xic_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the total XIC score" help=""/>
         <param name="use_total_mi_score" argument="-Scoring:Scores:use_total_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the total MI score" help=""/>
         <param name="use_sn_score" argument="-Scoring:Scores:use_sn_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the SN (signal to noise) score" help=""/>
-        <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MI (mutual information) score" help=""/>
+        <param name="use_mi_score" argument="-Scoring:Scores:use_mi_score" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MI (mutual information) score" help=""/>
         <param name="use_dia_scores" argument="-Scoring:Scores:use_dia_scores" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the DIA (SWATH) scores" help="If turned off, will not use fragment ion spectra for scoring"/>
         <param name="use_ms1_correlation" argument="-Scoring:Scores:use_ms1_correlation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the correlation scores with the MS1 elution profiles" help=""/>
         <param name="use_sonar_scores" argument="-Scoring:Scores:use_sonar_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for SONAR scans (scanning swath)" help=""/>
         <param name="use_ion_mobility_scores" argument="-Scoring:Scores:use_ion_mobility_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the scores for Ion Mobility scans" help=""/>
         <param name="use_ms1_fullscan" argument="-Scoring:Scores:use_ms1_fullscan" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help=""/>
-        <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the MS1 MI score" help=""/>
+        <param name="use_ms1_mi" argument="-Scoring:Scores:use_ms1_mi" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the MS1 MI score" help=""/>
         <param name="use_uis_scores" argument="-Scoring:Scores:use_uis_scores" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use UIS scores for peptidoform identification" help=""/>
       </section>
     </section>
     <expand macro="adv_opts_macro">
       <param name="rt_norm" argument="-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="If set, tr_irt may be omitted select trafoxml data sets(s)"/>
-      <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Optional, tab-separated file containing the SWATH windows for extraction: lower_offset upper_offset" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
       <param name="sort_swath_maps" argument="-sort_swath_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort input SWATH files when matching to SWATH windows from swath_windows_file" help=""/>
-      <param name="use_ms1_traces" argument="-use_ms1_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the precursor ion trace(s) and use for scoring" help=""/>
-      <param name="enable_uis_scoring" argument="-enable_uis_scoring" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable additional scoring of identification assays" help=""/>
+      <param name="enable_ms1" argument="-enable_ms1" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Extract the precursor ion trace(s) and use for scoring if present" help=""/>
+      <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable additional scoring of identification assays using IPF (see online documentation)" help=""/>
       <param name="out_chrom_type" type="select" optional="false" label="File type of output out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))">
         <option value="mzML">mzml</option>
         <option value="sqMass">sqmass</option>
@@ -347,21 +350,21 @@
       <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson" help=""/>
       <param name="extra_rt_extraction_window" argument="-extra_rt_extraction_window" type="float" optional="true" min="0.0" value="0.0" label="Output an XIC with a RT-window by this much large" help="(e.g. to visually inspect a larger area of the chromatogram)"/>
       <param name="mz_extraction_window_unit" argument="-mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
-        <option value="Th" selected="true">Th</option>
-        <option value="ppm">ppm</option>
+        <option value="Th">Th</option>
+        <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san"/>
       </param>
       <param name="mz_extraction_window_ms1_unit" argument="-mz_extraction_window_ms1_unit" display="radio" type="select" optional="false" label="Unit of the MS1 m/z extraction window" help="">
-        <option value="ppm">ppm</option>
-        <option value="Th" selected="true">Th</option>
+        <option value="ppm" selected="true">ppm</option>
+        <option value="Th">Th</option>
         <expand macro="list_string_san"/>
       </param>
       <param name="use_ms1_ion_mobility" argument="-use_ms1_ion_mobility" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Also perform precursor extraction using the same ion mobility window as for fragment ion extraction" help=""/>
       <param name="matching_window_only" argument="-matching_window_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume the input data is targeted / PRM-like data with potentially overlapping DIA windows" help="Will only attempt to extract each assay from the *best* matching DIA window (instead of all matching windows)"/>
-      <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
+      <param name="irt_mz_extraction_window" argument="-irt_mz_extraction_window" type="float" optional="true" min="0.0" value="50.0" label="Extraction window used for iRT and m/z correction in Thomson or ppm (see irt_mz_extraction_window_unit)" help=""/>
       <param name="irt_mz_extraction_window_unit" argument="-irt_mz_extraction_window_unit" display="radio" type="select" optional="false" label="Unit for mz extraction" help="">
-        <option value="Th" selected="true">Th</option>
-        <option value="ppm">ppm</option>
+        <option value="Th">Th</option>
+        <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san"/>
       </param>
       <param name="irt_im_extraction_window" argument="-irt_im_extraction_window" type="float" optional="true" value="-1.0" label="Ion mobility extraction window used for iRT (in 1/K0 or milliseconds)" help=""/>
@@ -392,21 +395,21 @@
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san"/>
       </param>
-      <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="250" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
-      <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="0" label="The number of MS1 isotopes used for extraction" help=""/>
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="batchSize" argument="-batchSize" type="integer" optional="true" min="0" value="1000" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 250-1000)" help=""/>
+      <param name="ms1_isotopes" argument="-ms1_isotopes" type="integer" optional="true" min="0" value="3" label="The number of MS1 isotopes used for extraction" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
-      <option value="out_features_FLAG">out_features (Use UIS scores for peptidoform identification)</option>
-      <option value="out_tsv_FLAG">out_tsv (Use UIS scores for peptidoform identification)</option>
-      <option value="out_osw_FLAG">out_osw (Use UIS scores for peptidoform identification)</option>
-      <option value="out_chrom_FLAG">out_chrom (Use UIS scores for peptidoform identification)</option>
-      <option value="out_qc_FLAG">out_qc (Use UIS scores for peptidoform identification)</option>
-      <option value="irt_mzml_FLAG">irt_mzml (Use UIS scores for peptidoform identification)</option>
-      <option value="irt_trafo_FLAG">irt_trafo (Use UIS scores for peptidoform identification)</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_features_FLAG">out_features (output file)</option>
+      <option value="out_tsv_FLAG">out_tsv (TSV output file (mProphet-compatible TSV file))</option>
+      <option value="out_osw_FLAG">out_osw (OSW output file (PyProphet-compatible SQLite file))</option>
+      <option value="out_chrom_FLAG">out_chrom (Also output all computed chromatograms output in mzML (chrom.mzML) or sqMass (SQLite format))</option>
+      <option value="out_qc_FLAG">out_qc (Optional QC meta data (charge distribution in MS1))</option>
+      <option value="irt_mzml_FLAG">irt_mzml (Chromatogram mzML containing the iRT peptides)</option>
+      <option value="irt_trafo_FLAG">irt_trafo (Transformation file for RT transform)</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
@@ -450,6 +453,6 @@
   <help><![CDATA[Complete workflow to run OpenSWATH
 
 
-For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathWorkflow.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_OpenSwathWorkflow.html]]></help>
   <expand macro="references"/>
 </tool>