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author | galaxyp |
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date | Wed, 13 May 2015 21:19:44 -0400 |
parents | 3070d71e0e5c |
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<?xml version='1.0' encoding='UTF-8'?> <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="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 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_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_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 name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/> <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> <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) "/> <param name="param_no_strict" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/> <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be used"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_min_upper_edge_dist" type="float" value="0.0" 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)" help="(-min_upper_edge_dist) "/> <param name="param_algorithm_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_algorithm_rt_extraction_window" type="float" value="-1.0" 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)" help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values"/> <param name="param_algorithm_rt_normalization_factor" type="float" value="1.0" 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_algorithm_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_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/> <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="legacy" 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_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/> <param name="param_algorithm_DIAScoring_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/> <param name="param_algorithm_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_algorithm_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_algorithm_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_algorithm_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_algorithm_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) "/> <expand macro="advanced_options"> <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> <param name="param_model_type" type="select" optional="True" value="linear" label="Type of model" help="(-type) "> <option value="linear">linear</option> <option value="b_spline">b_spline</option> <option value="interpolated">interpolated</option> </param> <param name="param_model_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/> <param name="param_algorithm_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_algorithm_write_convex_hull" type="boolean" truevalue="-algorithm: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_algorithm_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra) "/> <param name="param_algorithm_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling) "/> <param name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/> <param name="param_algorithm_TransitionGroupPicker_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that"> <option value="none">none</option> <option value="smoothed">smoothed</option> <option value="original">original</option> </param> <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" 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="""/> </valid> </sanitizer> </param> <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/> <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/> <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" 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="""/> </valid> </sanitizer> </param> <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/> <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/> <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/> <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/> <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/> <param name="param_algorithm_Scores_use_shape_score" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_coelution_score" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_rt_score" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/> <param name="param_algorithm_Scores_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score" falsevalue="" checked="true" optional="True" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score) "/> <param name="param_algorithm_Scores_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/> <param name="param_algorithm_Scores_use_nr_peaks_score" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/> <param name="param_algorithm_Scores_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/> <param name="param_algorithm_Scores_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/> <param name="param_algorithm_Scores_use_ms1_correlation" type="boolean" truevalue="-algorithm: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_algorithm_Scores_use_ms1_fullscan" type="boolean" truevalue="-algorithm: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" format="featurexml"/> </outputs> <help>**What it does** 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> <expand macro="references"/> </tool>