--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathWorkflow.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,358 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.0.0">
+  <description>Complete workflow to run OpenSWATH</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathWorkflow
+
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_tr:
+  -tr $param_tr
+#end if
+#if $param_tr_type:
+  -tr_type
+  #if " " in str($param_tr_type):
+    "$param_tr_type"
+  #else
+    $param_tr_type
+  #end if
+#end if
+#if $param_tr_irt:
+  -tr_irt $param_tr_irt
+#end if
+#if $param_out_features:
+  -out_features $param_out_features
+#end if
+#if $param_out_tsv:
+  -out_tsv     "$param_out_tsv"
+#end if
+#if $param_out_chrom:
+  -out_chrom $param_out_chrom
+#end if
+#if $param_rt_extraction_window:
+  -rt_extraction_window $param_rt_extraction_window
+#end if
+#if $param_mz_extraction_window:
+  -mz_extraction_window $param_mz_extraction_window
+#end if
+#if $param_ppm:
+  -ppm
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $param_Scoring_stop_report_after_feature:
+  -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
+#end if
+#if $param_Scoring_rt_normalization_factor:
+  -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
+#end if
+#if $param_Scoring_TransitionGroupPicker_stop_after_feature:
+  -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
+#end if
+#if $param_Scoring_TransitionGroupPicker_min_peak_width:
+  -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
+#end if
+#if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
+  -Scoring:TransitionGroupPicker:recalculate_peaks     "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
+#end if
+#if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
+  -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
+#end if
+#if $param_Scoring_TransitionGroupPicker_minimal_quality:
+  -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"
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss     "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss"
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
+#end if
+#if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($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
+#end if
+#if $param_Scoring_DIAScoring_dia_centroided:
+  -Scoring:DIAScoring:dia_centroided
+#end if
+#if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
+  -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
+#end if
+#if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
+  -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
+#end if
+#if $param_Scoring_DIAScoring_dia_nr_isotopes:
+  -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
+#end if
+#if $param_Scoring_DIAScoring_dia_nr_charges:
+  -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
+#end if
+#if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
+  -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
+#end if
+#if $param_Scoring_EMGScoring_max_iteration:
+  -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
+#end if
+#if $param_Scoring_EMGScoring_deltaRelError:
+  -Scoring:EMGScoring:deltaRelError $param_Scoring_EMGScoring_deltaRelError
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_rt_norm:
+  -rt_norm $adv_opts.param_rt_norm
+#end if
+    #if $adv_opts.param_swath_windows_file:
+  -swath_windows_file $adv_opts.param_swath_windows_file
+#end if
+    #if $adv_opts.param_sort_swath_maps:
+  -sort_swath_maps
+#end if
+    #if $adv_opts.param_use_ms1_traces:
+  -use_ms1_traces
+#end if
+    #if $adv_opts.param_min_upper_edge_dist:
+  -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
+#end if
+    #if $adv_opts.param_extra_rt_extraction_window:
+  -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
+#end if
+    #if $adv_opts.param_min_rsq:
+  -min_rsq $adv_opts.param_min_rsq
+#end if
+    #if $adv_opts.param_min_coverage:
+  -min_coverage $adv_opts.param_min_coverage
+#end if
+    #if $adv_opts.param_split_file_input:
+  -split_file_input
+#end if
+    #if $adv_opts.param_use_elution_model_score:
+  -use_elution_model_score
+#end if
+    #if $adv_opts.param_readOptions:
+  -readOptions
+  #if " " in str($adv_opts.param_readOptions):
+    "$adv_opts.param_readOptions"
+  #else
+    $adv_opts.param_readOptions
+  #end if
+#end if
+    #if $adv_opts.param_tempDirectory:
+  -tempDirectory     "$adv_opts.param_tempDirectory"
+#end if
+    #if $adv_opts.param_extraction_function:
+  -extraction_function
+  #if " " in str($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
+#end if
+    #if $adv_opts.param_force:
+  -force
+#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_Scores_use_shape_score:
+  -Scoring:Scores:use_shape_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_coelution_score:
+  -Scoring:Scores:use_coelution_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_rt_score:
+  -Scoring:Scores:use_rt_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_library_score:
+  -Scoring:Scores:use_library_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_intensity_score:
+  -Scoring:Scores:use_intensity_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
+  -Scoring:Scores:use_nr_peaks_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
+  -Scoring:Scores:use_total_xic_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_sn_score:
+  -Scoring:Scores:use_sn_score
+#end if
+    #if $adv_opts.param_Scoring_Scores_use_dia_scores:
+  -Scoring:Scores:use_dia_scores
+#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_ms1_fullscan:
+  -Scoring:Scores:use_ms1_fullscan
+#end if
+#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) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </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" 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>
+    </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" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
+    <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_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
+    <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
+    <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>
+    <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>
+    <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) "/>
+    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
+    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_Scoring_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_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" 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_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="true" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
+    <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
+      <option value="legacy">legacy</option>
+      <option value="corrected">corrected</option>
+      <option value="crawdad">crawdad</option>
+    </param>
+    <param name="param_Scoring_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
+    <param name="param_Scoring_DIAScoring_dia_centroided" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
+    <param name="param_Scoring_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/>
+    <param name="param_Scoring_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/>
+    <param name="param_Scoring_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
+    <param name="param_Scoring_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
+    <param name="param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help="(-peak_before_mono_max_ppm_diff) "/>
+    <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
+    <param name="param_Scoring_EMGScoring_deltaRelError" type="float" value="0.1" label="" help="(-deltaRelError) "/>
+    <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: 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" 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" 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_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
+      <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/>
+      <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
+      <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
+      <param name="param_split_file_input" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/>
+      <param name="param_use_elution_model_score" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/>
+      <param name="param_readOptions" type="select" optional="True" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory">
+        <option value="normal">normal</option>
+        <option value="cache">cache</option>
+      </param>
+      <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">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
+        <option value="tophat">tophat</option>
+        <option value="bartlett">bartlett</option>
+      </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" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <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" 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_Scores_use_shape_score" type="boolean" truevalue="-Scoring:Scores:use_shape_score" falsevalue="" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) "/>
+      <param name="param_Scoring_Scores_use_coelution_score" type="boolean" truevalue="-Scoring:Scores:use_coelution_score" falsevalue="" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) "/>
+      <param name="param_Scoring_Scores_use_rt_score" type="boolean" truevalue="-Scoring:Scores:use_rt_score" falsevalue="" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) "/>
+      <param name="param_Scoring_Scores_use_library_score" type="boolean" truevalue="-Scoring:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/>
+      <param name="param_Scoring_Scores_use_intensity_score" type="boolean" truevalue="-Scoring:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/>
+      <param name="param_Scoring_Scores_use_nr_peaks_score" type="boolean" truevalue="-Scoring:Scores:use_nr_peaks_score" falsevalue="" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score) "/>
+      <param name="param_Scoring_Scores_use_total_xic_score" type="boolean" truevalue="-Scoring:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/>
+      <param name="param_Scoring_Scores_use_sn_score" type="boolean" truevalue="-Scoring:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/>
+      <param name="param_Scoring_Scores_use_dia_scores" type="boolean" truevalue="-Scoring:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/>
+      <param name="param_Scoring_Scores_use_ms1_correlation" 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_ms1_fullscan" 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) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out_features" format="featurexml"/>
+    <data name="param_out_chrom" format="mzml"/>
+  </outputs>
+  <help>**What it does**
+
+Complete workflow to run OpenSWATH
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help>
+  <expand macro="references"/>
+</tool>