Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.8+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.6+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.3.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.1.0 |
OpenSwathRTNormalizer |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 2.6 | package |
openms-thirdparty | 2.6 | package |
blast | 2.9.0 | package |
ctdopts | 1.4 | package |
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: OpenSwathRTNormalizer_1_input.mzML tr: OpenSwathRTNormalizer_1_input.TraML min_rsq: 0.95 min_coverage: 0.6 estimateBestPeptides: False RTNormalization|outlierMethod: iter_residual RTNormalization|useIterativeChauvenet: False RTNormalization|RANSACMaxIterations: 1000 RTNormalization|RANSACMaxPercentRTThreshold: 3 RTNormalization|RANSACSamplingSize: 10 algorithm|stop_report_after_feature: -1 algorithm|rt_extraction_window: -1.0 algorithm|rt_normalization_factor: 1.0 algorithm|quantification_cutoff: 0.0 algorithm|write_convex_hull: False algorithm|spectrum_addition_method: simple algorithm|add_up_spectra: 1 algorithm|spacing_for_spectra_resampling: 0.005 algorithm|uis_threshold_sn: -1 algorithm|uis_threshold_peak_area: 0 algorithm|scoring_model: default algorithm|im_extra_drift: 0.0 algorithm|strict: true algorithm|TransitionGroupPicker|stop_after_feature: -1 algorithm|TransitionGroupPicker|stop_after_intensity_ratio: 0.0001 algorithm|TransitionGroupPicker|min_peak_width: -1.0 algorithm|TransitionGroupPicker|peak_integration: original algorithm|TransitionGroupPicker|background_subtraction: none algorithm|TransitionGroupPicker|recalculate_peaks: False algorithm|TransitionGroupPicker|use_precursors: False algorithm|TransitionGroupPicker|use_consensus: True algorithm|TransitionGroupPicker|recalculate_peaks_max_z: 1.0 algorithm|TransitionGroupPicker|minimal_quality: -10000.0 algorithm|TransitionGroupPicker|resample_boundary: 15.0 algorithm|TransitionGroupPicker|compute_peak_quality: False algorithm|TransitionGroupPicker|compute_peak_shape_metrics: False algorithm|TransitionGroupPicker|compute_total_mi: False algorithm|TransitionGroupPicker|boundary_selection_method: largest algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 15 algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3 algorithm|TransitionGroupPicker|PeakPickerMRM|gauss_width: 50.0 algorithm|TransitionGroupPicker|PeakPickerMRM|use_gauss: True algorithm|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_win_len: 1000.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_bin_count: 30 algorithm|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False algorithm|TransitionGroupPicker|PeakPickerMRM|method: corrected algorithm|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum algorithm|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base algorithm|TransitionGroupPicker|PeakIntegrator|fit_EMG: False algorithm|DIAScoring|dia_extraction_window: 0.05 algorithm|DIAScoring|dia_extraction_unit: Th algorithm|DIAScoring|dia_centroided: False algorithm|DIAScoring|dia_byseries_intensity_min: 300.0 algorithm|DIAScoring|dia_byseries_ppm_diff: 10.0 algorithm|DIAScoring|dia_nr_isotopes: 4 algorithm|DIAScoring|dia_nr_charges: 4 algorithm|DIAScoring|peak_before_mono_max_ppm_diff: 20.0 algorithm|EMGScoring|interpolation_step: 0.2 algorithm|EMGScoring|tolerance_stdev_bounding_box: 3.0 algorithm|EMGScoring|max_iteration: 500 algorithm|EMGScoring|statistics|mean: 1.0 algorithm|EMGScoring|statistics|variance: 1.0 algorithm|Scores|use_shape_score: True algorithm|Scores|use_coelution_score: True algorithm|Scores|use_rt_score: True algorithm|Scores|use_library_score: True algorithm|Scores|use_elution_model_score: True algorithm|Scores|use_intensity_score: True algorithm|Scores|use_nr_peaks_score: True algorithm|Scores|use_total_xic_score: True algorithm|Scores|use_total_mi_score: False algorithm|Scores|use_sn_score: True algorithm|Scores|use_mi_score: False algorithm|Scores|use_dia_scores: True algorithm|Scores|use_ms1_correlation: False algorithm|Scores|use_sonar_scores: False algorithm|Scores|use_ion_mobility_scores: False algorithm|Scores|use_ms1_fullscan: False algorithm|Scores|use_ms1_mi: False algorithm|Scores|use_uis_scores: False peptideEstimation|InitialQualityCutoff: 0.5 peptideEstimation|OverallQualityCutoff: 5.5 peptideEstimation|NrRTBins: 10 peptideEstimation|MinPeptidesPerBin: 1 peptideEstimation|MinBinsFilled: 8 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
OpenSwathRTNormalizer_1_input.mzML OpenSwathRTNormalizer_1_input.TraML value |
Test-2 |
in: OpenSwathRTNormalizer_1_input.mzML tr: OpenSwathRTNormalizer_1_input.TraML min_rsq: 0.95 min_coverage: 0.6 estimateBestPeptides: True RTNormalization|outlierMethod: iter_residual RTNormalization|useIterativeChauvenet: False RTNormalization|RANSACMaxIterations: 1000 RTNormalization|RANSACMaxPercentRTThreshold: 3 RTNormalization|RANSACSamplingSize: 10 algorithm|stop_report_after_feature: -1 algorithm|rt_extraction_window: -1.0 algorithm|rt_normalization_factor: 1.0 algorithm|quantification_cutoff: 0.0 algorithm|write_convex_hull: False algorithm|spectrum_addition_method: simple algorithm|add_up_spectra: 1 algorithm|spacing_for_spectra_resampling: 0.005 algorithm|uis_threshold_sn: -1 algorithm|uis_threshold_peak_area: 0 algorithm|scoring_model: default algorithm|im_extra_drift: 0.0 algorithm|strict: true algorithm|TransitionGroupPicker|stop_after_feature: -1 algorithm|TransitionGroupPicker|stop_after_intensity_ratio: 0.0001 algorithm|TransitionGroupPicker|min_peak_width: -1.0 algorithm|TransitionGroupPicker|peak_integration: original algorithm|TransitionGroupPicker|background_subtraction: none algorithm|TransitionGroupPicker|recalculate_peaks: False algorithm|TransitionGroupPicker|use_precursors: False algorithm|TransitionGroupPicker|use_consensus: True algorithm|TransitionGroupPicker|recalculate_peaks_max_z: 1.0 algorithm|TransitionGroupPicker|minimal_quality: -10000.0 algorithm|TransitionGroupPicker|resample_boundary: 15.0 algorithm|TransitionGroupPicker|compute_peak_quality: False algorithm|TransitionGroupPicker|compute_peak_shape_metrics: False algorithm|TransitionGroupPicker|compute_total_mi: False algorithm|TransitionGroupPicker|boundary_selection_method: largest algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 15 algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3 algorithm|TransitionGroupPicker|PeakPickerMRM|gauss_width: 50.0 algorithm|TransitionGroupPicker|PeakPickerMRM|use_gauss: True algorithm|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_win_len: 1000.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_bin_count: 30 algorithm|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False algorithm|TransitionGroupPicker|PeakPickerMRM|method: corrected algorithm|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum algorithm|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base algorithm|TransitionGroupPicker|PeakIntegrator|fit_EMG: False algorithm|DIAScoring|dia_extraction_window: 0.05 algorithm|DIAScoring|dia_extraction_unit: Th algorithm|DIAScoring|dia_centroided: False algorithm|DIAScoring|dia_byseries_intensity_min: 300.0 algorithm|DIAScoring|dia_byseries_ppm_diff: 10.0 algorithm|DIAScoring|dia_nr_isotopes: 4 algorithm|DIAScoring|dia_nr_charges: 4 algorithm|DIAScoring|peak_before_mono_max_ppm_diff: 20.0 algorithm|EMGScoring|interpolation_step: 0.2 algorithm|EMGScoring|tolerance_stdev_bounding_box: 3.0 algorithm|EMGScoring|max_iteration: 500 algorithm|EMGScoring|statistics|mean: 1.0 algorithm|EMGScoring|statistics|variance: 1.0 algorithm|Scores|use_shape_score: True algorithm|Scores|use_coelution_score: True algorithm|Scores|use_rt_score: True algorithm|Scores|use_library_score: True algorithm|Scores|use_elution_model_score: True algorithm|Scores|use_intensity_score: True algorithm|Scores|use_nr_peaks_score: True algorithm|Scores|use_total_xic_score: True algorithm|Scores|use_total_mi_score: False algorithm|Scores|use_sn_score: True algorithm|Scores|use_mi_score: False algorithm|Scores|use_dia_scores: True algorithm|Scores|use_ms1_correlation: False algorithm|Scores|use_sonar_scores: False algorithm|Scores|use_ion_mobility_scores: False algorithm|Scores|use_ms1_fullscan: False algorithm|Scores|use_ms1_mi: False algorithm|Scores|use_uis_scores: False peptideEstimation|InitialQualityCutoff: 0.5 peptideEstimation|OverallQualityCutoff: 5.5 peptideEstimation|NrRTBins: 3 peptideEstimation|MinPeptidesPerBin: 1 peptideEstimation|MinBinsFilled: 3 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
OpenSwathRTNormalizer_1_input.mzML OpenSwathRTNormalizer_1_input.TraML value |
Test-3 |
in: OpenSwathRTNormalizer_1_input.mzML tr: OpenSwathRTNormalizer_1_input.TraML min_rsq: 0.95 min_coverage: 0.6 estimateBestPeptides: False RTNormalization|outlierMethod: iter_residual RTNormalization|useIterativeChauvenet: False RTNormalization|RANSACMaxIterations: 1000 RTNormalization|RANSACMaxPercentRTThreshold: 3 RTNormalization|RANSACSamplingSize: 10 algorithm|stop_report_after_feature: -1 algorithm|rt_extraction_window: -1.0 algorithm|rt_normalization_factor: 1.0 algorithm|quantification_cutoff: 0.0 algorithm|write_convex_hull: False algorithm|spectrum_addition_method: simple algorithm|add_up_spectra: 1 algorithm|spacing_for_spectra_resampling: 0.005 algorithm|uis_threshold_sn: -1 algorithm|uis_threshold_peak_area: 0 algorithm|scoring_model: default algorithm|im_extra_drift: 0.0 algorithm|strict: true algorithm|TransitionGroupPicker|stop_after_feature: -1 algorithm|TransitionGroupPicker|stop_after_intensity_ratio: 0.0001 algorithm|TransitionGroupPicker|min_peak_width: -1.0 algorithm|TransitionGroupPicker|peak_integration: original algorithm|TransitionGroupPicker|background_subtraction: none algorithm|TransitionGroupPicker|recalculate_peaks: False algorithm|TransitionGroupPicker|use_precursors: False algorithm|TransitionGroupPicker|use_consensus: True algorithm|TransitionGroupPicker|recalculate_peaks_max_z: 1.0 algorithm|TransitionGroupPicker|minimal_quality: -10000.0 algorithm|TransitionGroupPicker|resample_boundary: 15.0 algorithm|TransitionGroupPicker|compute_peak_quality: False algorithm|TransitionGroupPicker|compute_peak_shape_metrics: False algorithm|TransitionGroupPicker|compute_total_mi: False algorithm|TransitionGroupPicker|boundary_selection_method: largest algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_frame_length: 15 algorithm|TransitionGroupPicker|PeakPickerMRM|sgolay_polynomial_order: 3 algorithm|TransitionGroupPicker|PeakPickerMRM|gauss_width: 50.0 algorithm|TransitionGroupPicker|PeakPickerMRM|use_gauss: True algorithm|TransitionGroupPicker|PeakPickerMRM|peak_width: -1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|signal_to_noise: 1.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_win_len: 1000.0 algorithm|TransitionGroupPicker|PeakPickerMRM|sn_bin_count: 30 algorithm|TransitionGroupPicker|PeakPickerMRM|write_sn_log_messages: False algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False algorithm|TransitionGroupPicker|PeakPickerMRM|method: corrected algorithm|TransitionGroupPicker|PeakIntegrator|integration_type: intensity_sum algorithm|TransitionGroupPicker|PeakIntegrator|baseline_type: base_to_base algorithm|TransitionGroupPicker|PeakIntegrator|fit_EMG: False algorithm|DIAScoring|dia_extraction_window: 0.05 algorithm|DIAScoring|dia_extraction_unit: Th algorithm|DIAScoring|dia_centroided: False algorithm|DIAScoring|dia_byseries_intensity_min: 300.0 algorithm|DIAScoring|dia_byseries_ppm_diff: 10.0 algorithm|DIAScoring|dia_nr_isotopes: 4 algorithm|DIAScoring|dia_nr_charges: 4 algorithm|DIAScoring|peak_before_mono_max_ppm_diff: 20.0 algorithm|EMGScoring|interpolation_step: 0.2 algorithm|EMGScoring|tolerance_stdev_bounding_box: 3.0 algorithm|EMGScoring|max_iteration: 500 algorithm|EMGScoring|statistics|mean: 1.0 algorithm|EMGScoring|statistics|variance: 1.0 algorithm|Scores|use_shape_score: True algorithm|Scores|use_coelution_score: True algorithm|Scores|use_rt_score: True algorithm|Scores|use_library_score: True algorithm|Scores|use_elution_model_score: True algorithm|Scores|use_intensity_score: True algorithm|Scores|use_nr_peaks_score: True algorithm|Scores|use_total_xic_score: True algorithm|Scores|use_total_mi_score: False algorithm|Scores|use_sn_score: True algorithm|Scores|use_mi_score: False algorithm|Scores|use_dia_scores: True algorithm|Scores|use_ms1_correlation: False algorithm|Scores|use_sonar_scores: False algorithm|Scores|use_ion_mobility_scores: False algorithm|Scores|use_ms1_fullscan: False algorithm|Scores|use_ms1_mi: False algorithm|Scores|use_uis_scores: False peptideEstimation|InitialQualityCutoff: 0.5 peptideEstimation|OverallQualityCutoff: 5.5 peptideEstimation|NrRTBins: 10 peptideEstimation|MinPeptidesPerBin: 1 peptideEstimation|MinBinsFilled: 8 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
OpenSwathRTNormalizer_1_input.mzML OpenSwathRTNormalizer_1_input.TraML value |