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view OpenSwathAnalyzer.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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<?xml version="1.0" encoding="UTF-8"?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [Targeted Experiments]--> <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.0.0"> <description>Picks peaks and finds features in an SRM experiment.</description> <macros> <token name="@EXECUTABLE@">OpenSwathAnalyzer</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>OpenSwathAnalyzer #if $param_in: -in $param_in #end if #if $param_tr: -tr $param_tr #end if #if $param_rt_norm: -rt_norm $param_rt_norm #end if #if $param_out: -out $param_out #end if #if $param_no_strict: -no-strict #end if -swath_files #for token in $param_swath_files: $token #end for #if $param_min_upper_edge_dist: -min_upper_edge_dist $param_min_upper_edge_dist #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_stop_report_after_feature: -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature #end if #if $param_algorithm_rt_extraction_window: -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window #end if #if $param_algorithm_rt_normalization_factor: -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor #end if #if $param_algorithm_TransitionGroupPicker_stop_after_feature: -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature #end if #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio: -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length: -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order: -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width: -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise: -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len: -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count: -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: -algorithm:TransitionGroupPicker:PeakPickerMRM:method #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method): "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" #else $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method #end if #end if #if $param_algorithm_DIAScoring_dia_extraction_window: -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window #end if #if $param_algorithm_DIAScoring_dia_centroided: -algorithm:DIAScoring:dia_centroided #end if #if $param_algorithm_DIAScoring_dia_byseries_intensity_min: -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min #end if #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff: -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff #end if #if $param_algorithm_DIAScoring_dia_nr_isotopes: -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes #end if #if $param_algorithm_DIAScoring_dia_nr_charges: -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges #end if #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff: -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_model_type: -model:type #if " " in str($adv_opts.param_model_type): "$adv_opts.param_model_type" #else $adv_opts.param_model_type #end if #end if #if $adv_opts.param_model_symmetric_regression: -model:symmetric_regression #end if #if $adv_opts.param_algorithm_quantification_cutoff: -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff #end if #if $adv_opts.param_algorithm_write_convex_hull: -algorithm:write_convex_hull #end if #if $adv_opts.param_algorithm_add_up_spectra: -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra #end if #if $adv_opts.param_algorithm_spacing_for_spectra_resampling: -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width: -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: -algorithm:TransitionGroupPicker:background_subtraction #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction): "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction" #else $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction #end if #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z: -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality: -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality: -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality" #end if #if $adv_opts.param_algorithm_EMGScoring_interpolation_step: -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step #end if #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box: -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box #end if #if $adv_opts.param_algorithm_EMGScoring_max_iteration: -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration #end if #if $adv_opts.param_algorithm_EMGScoring_statistics_mean: -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean #end if #if $adv_opts.param_algorithm_EMGScoring_statistics_variance: -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance #end if #if $adv_opts.param_algorithm_Scores_use_shape_score: -algorithm:Scores:use_shape_score #end if #if $adv_opts.param_algorithm_Scores_use_coelution_score: -algorithm:Scores:use_coelution_score #end if #if $adv_opts.param_algorithm_Scores_use_rt_score: -algorithm:Scores:use_rt_score #end if #if $adv_opts.param_algorithm_Scores_use_library_score: -algorithm:Scores:use_library_score #end if #if $adv_opts.param_algorithm_Scores_use_elution_model_score: -algorithm:Scores:use_elution_model_score #end if #if $adv_opts.param_algorithm_Scores_use_intensity_score: -algorithm:Scores:use_intensity_score #end if #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: -algorithm:Scores:use_nr_peaks_score #end if #if $adv_opts.param_algorithm_Scores_use_total_xic_score: -algorithm:Scores:use_total_xic_score #end if #if $adv_opts.param_algorithm_Scores_use_sn_score: -algorithm:Scores:use_sn_score #end if #if $adv_opts.param_algorithm_Scores_use_dia_scores: -algorithm:Scores:use_dia_scores #end if #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: -algorithm:Scores:use_ms1_correlation #end if #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan: -algorithm:Scores:use_ms1_fullscan #end if #end if </command> <inputs> <param format="mzml" help="(-in) " label="input file containing the chromatograms" name="param_in" optional="False" type="data"/> <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/> <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/> <param checked="false" falsevalue="" help="(-no-strict) " label="run in non-strict mode and allow some chromatograms to not be mapped" name="param_no_strict" optional="True" truevalue="-no-strict" type="boolean"/> <param format="mzml" help="(-swath_files) If present, SWATH specific scoring will be used" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" multiple="true" name="param_swath_files" optional="True" size="30" type="data"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-min_upper_edge_dist) " label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" name="param_min_upper_edge_dist" type="float" value="0.0"/> <param help="(-stop_report_after_feature) " label="Stop reporting after feature (ordered by quality; -1 means do not stop)" name="param_algorithm_stop_report_after_feature" type="integer" value="-1"/> <param help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" name="param_algorithm_rt_extraction_window" type="float" value="-1.0"/> <param help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" name="param_algorithm_rt_normalization_factor" type="float" value="1.0"/> <param help="(-stop_after_feature) " label="Stop finding after feature (ordered by intensity; -1 means do not stop)" name="param_algorithm_TransitionGroupPicker_stop_after_feature" type="integer" value="-1"/> <param help="(-stop_after_intensity_ratio) " label="Stop after reaching intensity ratio" name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001"/> <param help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added" label="The number of subsequent data points used for smoothing" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15"/> <param help="(-sgolay_polynomial_order) " label="Order of the polynomial that is fitted" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3"/> <param help="(-gauss_width) " label="Gaussian width in seconds, estimated peak size" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0"/> <param checked="true" falsevalue="" help="(-use_gauss) " label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss" type="boolean"/> <param help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off" label="Force a certain minimal peak_width on the data (" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0"/> <param help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" min="0.0" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" optional="True" type="float" value="1.0"/> <param help="(-sn_win_len) " label="Signal to noise window length" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0"/> <param help="(-sn_bin_count) " label="Signal to noise bin count" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30"/> <param checked="true" falsevalue="" help="(-write_sn_log_messages) " label="Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages" type="boolean"/> <param checked="false" falsevalue="" help="(-remove_overlapping_peaks) " label="Try to remove overlapping peaks during peak picking" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" optional="True" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" type="boolean"/> <param help="(-method) " label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" optional="True" type="select" value="legacy"> <option value="legacy">legacy</option> <option value="corrected">corrected</option> <option value="crawdad">crawdad</option> </param> <param help="(-dia_extraction_window) " label="DIA extraction window in Th" min="0.0" name="param_algorithm_DIAScoring_dia_extraction_window" optional="True" type="float" value="0.05"/> <param checked="false" falsevalue="" help="(-dia_centroided) " label="Use centroded DIA data" name="param_algorithm_DIAScoring_dia_centroided" optional="True" truevalue="-algorithm:DIAScoring:dia_centroided" type="boolean"/> <param help="(-dia_byseries_intensity_min) " label="DIA b/y series minimum intensity to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_intensity_min" optional="True" type="float" value="300.0"/> <param help="(-dia_byseries_ppm_diff) " label="DIA b/y series minimal difference in ppm to conside" min="0.0" name="param_algorithm_DIAScoring_dia_byseries_ppm_diff" optional="True" type="float" value="10.0"/> <param help="(-dia_nr_isotopes) " label="DIA nr of isotopes to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_isotopes" optional="True" type="integer" value="4"/> <param help="(-dia_nr_charges) " label="DIA nr of charges to conside" min="0" name="param_algorithm_DIAScoring_dia_nr_charges" optional="True" type="integer" value="4"/> <param help="(-peak_before_mono_max_ppm_diff) " 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" min="0.0" name="param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff" optional="True" type="float" value="20.0"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear"> <option value="linear">linear</option> <option value="b_spline">b_spline</option> <option value="interpolated">interpolated</option> </param> <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/> <param help="(-quantification_cutoff) " label="Cutoff in m/z below which peaks should not be used for quantification any more" min="0.0" name="param_algorithm_quantification_cutoff" optional="True" type="float" value="0.0"/> <param checked="false" falsevalue="" help="(-write_convex_hull) " label="Whether to write out all points of all features into the featureXML" name="param_algorithm_write_convex_hull" optional="True" truevalue="-algorithm:write_convex_hull" type="boolean"/> <param help="(-add_up_spectra) " label="Add up spectra around the peak apex (needs to be a non-even integer)" min="1" name="param_algorithm_add_up_spectra" optional="True" type="integer" value="1"/> <param help="(-spacing_for_spectra_resampling) " label="If spectra are to be added, use this spacing to add them up" min="0.0" name="param_algorithm_spacing_for_spectra_resampling" optional="True" type="float" value="0.005"/> <param help="(-min_peak_width) " label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0"/> <param help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that" label="Try to apply a background subtraction to the peak (experimental)" name="param_algorithm_TransitionGroupPicker_background_subtraction" optional="True" type="select" value="none"> <option value="none">none</option> <option value="smoothed">smoothed</option> <option value="original">original</option> </param> <param help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" name="param_algorithm_TransitionGroupPicker_recalculate_peaks" size="30" type="text" value="false"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0"/> <param help="(-minimal_quality) " label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0"/> <param 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" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" name="param_algorithm_TransitionGroupPicker_compute_peak_quality" size="30" type="text" value="false"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-interpolation_step) " label="Sampling rate for the interpolation of the model function" name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2"/> <param help="(-tolerance_stdev_bounding_box) " label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0"/> <param help="(-max_iteration) " label="Maximum number of iterations using by Levenberg-Marquardt algorithm" name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500"/> <param help="(-mean) " label="Centroid position of the model" name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0"/> <param help="(-variance) " label="Variance of the model" name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0"/> <param checked="true" falsevalue="" help="(-use_shape_score) " label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_shape_score" optional="True" truevalue="-algorithm:Scores:use_shape_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_coelution_score) " label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" name="param_algorithm_Scores_use_coelution_score" optional="True" truevalue="-algorithm:Scores:use_coelution_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_rt_score) " label="Use the retention time score (this score measure the difference in retention time)" name="param_algorithm_Scores_use_rt_score" optional="True" truevalue="-algorithm:Scores:use_rt_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_library_score) " label="Use the library score" name="param_algorithm_Scores_use_library_score" optional="True" truevalue="-algorithm:Scores:use_library_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_elution_model_score) " label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" name="param_algorithm_Scores_use_elution_model_score" optional="True" truevalue="-algorithm:Scores:use_elution_model_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_intensity_score) " label="Use the intensity score" name="param_algorithm_Scores_use_intensity_score" optional="True" truevalue="-algorithm:Scores:use_intensity_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_nr_peaks_score) " label="Use the number of peaks score" name="param_algorithm_Scores_use_nr_peaks_score" optional="True" truevalue="-algorithm:Scores:use_nr_peaks_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_total_xic_score) " label="Use the total XIC score" name="param_algorithm_Scores_use_total_xic_score" optional="True" truevalue="-algorithm:Scores:use_total_xic_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_sn_score) " label="Use the SN (signal to noise) score" name="param_algorithm_Scores_use_sn_score" optional="True" truevalue="-algorithm:Scores:use_sn_score" type="boolean"/> <param checked="true" falsevalue="" help="(-use_dia_scores) " label="Use the DIA (SWATH) scores" name="param_algorithm_Scores_use_dia_scores" optional="True" truevalue="-algorithm:Scores:use_dia_scores" type="boolean"/> <param checked="false" falsevalue="" help="(-use_ms1_correlation) " label="Use the correlation scores with the MS1 elution profiles" name="param_algorithm_Scores_use_ms1_correlation" optional="True" truevalue="-algorithm:Scores:use_ms1_correlation" type="boolean"/> <param checked="false" falsevalue="" help="(-use_ms1_fullscan) " label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" name="param_algorithm_Scores_use_ms1_fullscan" optional="True" truevalue="-algorithm:Scores:use_ms1_fullscan" type="boolean"/> </expand> </inputs> <outputs> <data format="xml" name="param_out"/> </outputs> <help>Picks peaks and finds features in an SRM experiment. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help> </tool>