Repository revision
12:6e8cc5ed2a9b

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

OpenSwathRTNormalizer tool metadata
Miscellaneous
This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space.
OpenSwathRTNormalizer
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathrtnormalizer/OpenSwathRTNormalizer/2.6+galaxy0
2.6+galaxy0
None
True
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