Repository revision
10:887be35bc42e

Repository 'openms_openswathworkflow'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow

OpenSwathWorkflow tool metadata
Miscellaneous
OpenSwathWorkflow
Complete workflow to run OpenSWATH
OpenSwathWorkflow
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0
2.5+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.2.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathworkflow/OpenSwathWorkflow/2.1.0
OpenSwathWorkflow
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.5 package
openms-thirdparty 2.5 package
blast 2.9.0 package
openjdk 8.0.192 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: False
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG', 'out_qc_FLAG']
 name: value
name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-2 in: OpenSwathWorkflow_2_input.mzXML
tr: OpenSwathWorkflow_2_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_2_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: False
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_2_input.mzXML
OpenSwathWorkflow_2_input.TraML
OpenSwathWorkflow_2_input.trafoXML
value
Test-3 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-4 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_tsv_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-5 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: cache
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-6 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: cacheWorkingInMemory
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-7 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|swath_windows_file: swath_windows.txt
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
swath_windows.txt
value
Test-8 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|swath_windows_file: swath_windows_overlap.txt
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: True
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
swath_windows_overlap.txt
value
Test-9 in: OpenSwathWorkflow_11_input.mzML
tr: OpenSwathWorkflow_11_input_2.TraML
tr_irt: OpenSwathWorkflow_11_input.TraML
sonar: True
rt_extraction_window: -1.0
ion_mobility_window: -1.0
mz_extraction_window: 0.2
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: none
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: True
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: False
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 550.0
adv_opts_cond|irt_mz_extraction_window_unit: ppm
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: quadratic_regression_delta_ppm
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_11_input.mzML
OpenSwathWorkflow_11_input_2.TraML
OpenSwathWorkflow_11_input.TraML
value
Test-10 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_13_input.pqp.tmp
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_osw_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_13_input.pqp.tmp
OpenSwathWorkflow_1_input.trafoXML
value
Test-11 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_14_input.pqp.tmp
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: sqMass
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_osw_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_14_input.pqp.tmp
OpenSwathWorkflow_1_input.trafoXML
value
Test-12 in: OpenSwathWorkflow_15_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: True
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: False
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 2
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_15_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-13 in: OpenSwathWorkflow_16_input.sqMass
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: workingInMemory
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 2
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_16_input.sqMass
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-14 in: OpenSwathWorkflow_17_input.mzML
tr: OpenSwathWorkflow_17_input.tsv
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: 0.05
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: True
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: False
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: workingInMemory
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_17_input.mzML
OpenSwathWorkflow_17_input.tsv
value
Test-15 in: OpenSwathWorkflow_17_input.mzML
tr: OpenSwathWorkflow_17_input.tsv
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: 0.05
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: True
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: False
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: cache
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_17_input.mzML
OpenSwathWorkflow_17_input.tsv
value
Test-16 in: OpenSwathWorkflow_17_input.mzML
tr: OpenSwathWorkflow_17_input.pqp.tmp
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: 0.05
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: False
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: workingInMemory
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_17_input.mzML
OpenSwathWorkflow_17_input.pqp.tmp
value
Test-17 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: True
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG']
 name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-18 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: True
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG']
 name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-19 in: OpenSwathWorkflow_1_input.mzML
tr: OpenSwathWorkflow_1_input.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: True
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: True
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|rt_norm: OpenSwathWorkflow_1_input.trafoXML
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG']
 name: value
name: value
 OpenSwathWorkflow_1_input.mzML
OpenSwathWorkflow_1_input.TraML
OpenSwathWorkflow_1_input.trafoXML
value
Test-20 in: OpenSwathWorkflow_21_input.mzML
tr: OpenSwathWorkflow_21_input.tsv
tr_irt: OpenSwathWorkflow_21_input.irt.TraML
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: True
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: True
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: False
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: normal
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG', 'irt_trafo_FLAG']
 name: value
name: value
name: value
name: value
 OpenSwathWorkflow_21_input.mzML
OpenSwathWorkflow_21_input.tsv
OpenSwathWorkflow_21_input.irt.TraML
value
Test-21 in: OpenSwathWorkflow_22_input.mzML
tr: OpenSwathWorkflow_22_input.tsv
sonar: False
rt_extraction_window: 600.0
ion_mobility_window: -1.0
mz_extraction_window: 0.05
mz_extraction_window_ms1: 0.05
im_extraction_window_ms1: -1.0
Calibration|ms1_im_calibration: False
Calibration|im_correction_function: linear
Calibration|debug_im_file:
Calibration|debug_mz_file:
Library|retentionTimeInterpretation: iRT
Library|override_group_label_check: False
Library|force_invalid_mods: False
RTNormalization|alignmentMethod: linear
RTNormalization|outlierMethod: iter_residual
RTNormalization|useIterativeChauvenet: False
RTNormalization|RANSACMaxIterations: 1000
RTNormalization|RANSACMaxPercentRTThreshold: 3
RTNormalization|RANSACSamplingSize: 10
RTNormalization|estimateBestPeptides: False
RTNormalization|InitialQualityCutoff: 0.5
RTNormalization|OverallQualityCutoff: 5.5
RTNormalization|NrRTBins: 10
RTNormalization|MinPeptidesPerBin: 1
RTNormalization|MinBinsFilled: 8
RTNormalization|lowess|span: 0.666666666666667
RTNormalization|b_spline|num_nodes: 5
Scoring|stop_report_after_feature: 5
Scoring|rt_normalization_factor: 100.0
Scoring|quantification_cutoff: 0.0
Scoring|write_convex_hull: False
Scoring|spectrum_addition_method: simple
Scoring|add_up_spectra: 1
Scoring|spacing_for_spectra_resampling: 0.005
Scoring|uis_threshold_sn: 0
Scoring|uis_threshold_peak_area: 0
Scoring|scoring_model: default
Scoring|im_extra_drift: 0.0
Scoring|TransitionGroupPicker|stop_after_feature: -1
Scoring|TransitionGroupPicker|min_peak_width: -1.0
Scoring|TransitionGroupPicker|peak_integration: original
Scoring|TransitionGroupPicker|background_subtraction: none
Scoring|TransitionGroupPicker|recalculate_peaks: True
Scoring|TransitionGroupPicker|use_precursors: False
Scoring|TransitionGroupPicker|use_consensus: True
Scoring|TransitionGroupPicker|recalculate_peaks_max_z: 0.75
Scoring|TransitionGroupPicker|minimal_quality: -1.5
Scoring|TransitionGroupPicker|resample_boundary: 15.0
Scoring|TransitionGroupPicker|compute_peak_quality: True
Scoring|TransitionGroupPicker|compute_peak_shape_metrics: False
Scoring|TransitionGroupPicker|compute_total_mi: False
Scoring|TransitionGroupPicker|boundary_selection_method: largest
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 11
Scoring|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3
Scoring|TransitionGroupPicker|PeakPickerMRM|gauss_width: 30.0
Scoring|TransitionGroupPicker|PeakPickerMRM|use_gauss: False
Scoring|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0
Scoring|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 0.1
Scoring|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False
Scoring|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: True
Scoring|TransitionGroupPicker|PeakPickerMRM|method: corrected
Scoring|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum
Scoring|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base
Scoring|TransitionGroupPicker|PeakIntegrator|fit_EMG: False
Scoring|DIAScoring|dia_extraction_window: 0.05
Scoring|DIAScoring|dia_extraction_unit: Th
Scoring|DIAScoring|dia_centroided: False
Scoring|DIAScoring|dia_byseries_intensity_min: 300.0
Scoring|DIAScoring|dia_byseries_ppm_diff: 10.0
Scoring|DIAScoring|dia_nr_isotopes: 4
Scoring|DIAScoring|dia_nr_charges: 4
Scoring|DIAScoring|peak_before_mono_max_ppm_diff: 20.0
Scoring|EMGScoring|max_iteration: 10
Scoring|Scores|use_shape_score: True
Scoring|Scores|use_coelution_score: True
Scoring|Scores|use_rt_score: True
Scoring|Scores|use_library_score: True
Scoring|Scores|use_intensity_score: True
Scoring|Scores|use_nr_peaks_score: True
Scoring|Scores|use_total_xic_score: True
Scoring|Scores|use_total_mi_score: False
Scoring|Scores|use_sn_score: True
Scoring|Scores|use_mi_score: False
Scoring|Scores|use_dia_scores: True
Scoring|Scores|use_ms1_correlation: False
Scoring|Scores|use_sonar_scores: False
Scoring|Scores|use_ion_mobility_scores: False
Scoring|Scores|use_ms1_fullscan: False
Scoring|Scores|use_ms1_mi: False
Scoring|Scores|use_uis_scores: False
adv_opts_cond|sort_swath_maps: False
adv_opts_cond|use_ms1_traces: True
adv_opts_cond|enable_uis_scoring: False
adv_opts_cond|out_chrom_type: mzML
adv_opts_cond|min_upper_edge_dist: 0.0
adv_opts_cond|extra_rt_extraction_window: 0.0
adv_opts_cond|mz_extraction_window_unit: Th
adv_opts_cond|mz_extraction_window_ms1_unit: Th
adv_opts_cond|use_ms1_ion_mobility: True
adv_opts_cond|matching_window_only: True
adv_opts_cond|irt_mz_extraction_window: 0.05
adv_opts_cond|irt_mz_extraction_window_unit: Th
adv_opts_cond|irt_im_extraction_window: -1.0
adv_opts_cond|min_rsq: 0.95
adv_opts_cond|min_coverage: 0.6
adv_opts_cond|split_file_input: False
adv_opts_cond|use_elution_model_score: False
adv_opts_cond|readOptions: workingInMemory
adv_opts_cond|mz_correction_function: none
adv_opts_cond|extraction_function: tophat
adv_opts_cond|batchSize: 250
adv_opts_cond|ms1_isotopes: 3
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_features_FLAG', 'out_chrom_FLAG']
 name: value
name: value
name: value
 OpenSwathWorkflow_22_input.mzML
OpenSwathWorkflow_22_input.tsv
value