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Revision: 10:4da16805dea6

Repository 'openms_openswathanalyzer'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer

OpenSwathAnalyzer tool metadata

Miscellaneous

Name: OpenSwathAnalyzer

Description: Picks peaks and finds features in an SWATH-MS or SRM experiment.

Id: OpenSwathAnalyzer

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.5+galaxy0

Version: 2.5+galaxy0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.6+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.5+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.3.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.2.0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathanalyzer/OpenSwathAnalyzer/2.1.0

OpenSwathAnalyzer

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

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: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
rt_norm: OpenSwathAnalyzer_input.trafoXML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_input.trafoXML
value

Test-2

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
no_strict: False
swath_files: OpenSwathAnalyzer_2_swathfile.mzML
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_2_swathfile.mzML
value

Test-3

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_mod_input.TraML
no_strict: False
swath_files: OpenSwathAnalyzer_2_swathfile.mzML
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: True
algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False
algorithm|TransitionGroupPicker|PeakPickerMRM|method: legacy
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: 8.0
algorithm|DIAScoring|dia_byseries_ppm_diff: 15.0
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_mod_input.TraML
OpenSwathAnalyzer_2_swathfile.mzML
value

Test-4

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
no_strict: False
swath_files: OpenSwathAnalyzer_2_swathfile.mzML
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: True
algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False
algorithm|TransitionGroupPicker|PeakPickerMRM|method: legacy
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: 8.0
algorithm|DIAScoring|dia_byseries_ppm_diff: 15.0
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_2_swathfile.mzML
value

Test-5

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: original
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: 40.0
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: True
algorithm|TransitionGroupPicker|PeakPickerMRM|remove_overlapping_peaks: False
algorithm|TransitionGroupPicker|PeakPickerMRM|method: legacy
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
value

Test-6

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
rt_norm: OpenSwathAnalyzer_input.trafoXML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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: True
algorithm|Scores|use_sn_score: True
algorithm|Scores|use_mi_score: True
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: True
algorithm|Scores|use_uis_scores: False
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_input.trafoXML
value

Test-7

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
rt_norm: OpenSwathAnalyzer_input.trafoXML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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: True
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_input.trafoXML
value

Test-8

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
rt_norm: OpenSwathAnalyzer_input.trafoXML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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: True
algorithm|Scores|use_sn_score: True
algorithm|Scores|use_mi_score: True
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_input.trafoXML
value

Test-9

in: OpenSwathAnalyzer_1_input_chrom.mzML
tr: OpenSwathAnalyzer_1_input.TraML
rt_norm: OpenSwathAnalyzer_input.trafoXML
no_strict: False
min_upper_edge_dist: 0.0
model|type: linear
model|symmetric_regression: False
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|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: 40.0
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: legacy
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: True
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
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

OpenSwathAnalyzer_1_input_chrom.mzML
OpenSwathAnalyzer_1_input.TraML
OpenSwathAnalyzer_input.trafoXML
value