| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.8+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.6+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.5+galaxy0 |
| AssayGeneratorMetabo |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| openms | 2.8 | package |
| openms-thirdparty | 2.8 | package |
| omssa | 2.1.9 | package |
| blast | 2.13.0 | package |
| ctdopts | 1.4 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
| Test-2 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-3 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
| Test-4 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-5 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-6 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-7 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: ALL fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-8 |
in_cond|in: AssayGeneratorMetabo_intsort_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_intsort_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_intsort_input.mzML AssayGeneratorMetabo_intsort_input.featureXML value |
| Test-9 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-10 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 3 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-11 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
| Test-12 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: resolve_overlap method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
| Test-13 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: add_shift method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
| Test-14 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
| Test-15 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input_multids.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_multids.featureXML value |
| Test-16 |
in_cond|in: ['AssayGeneratorMetabo_decoy_generation_input.mzML', 'AssayGeneratorMetabo_decoy_generation_input_2.mzML', 'AssayGeneratorMetabo_decoy_generation_input_3.mzML'] in_id_cond|in_id: ['AssayGeneratorMetabo_decoy_generation_input.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_1.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_2.featureXML'] out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.8 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 6 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: Da adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_2.mzML AssayGeneratorMetabo_decoy_generation_input_3.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML AssayGeneratorMetabo_decoy_generation_input_1.featureXML AssayGeneratorMetabo_decoy_generation_input_2.featureXML value |
| Test-17 |
in_cond|in: ['AssayGeneratorMetabo_decoy_generation_input.mzML', 'AssayGeneratorMetabo_decoy_generation_input_2.mzML', 'AssayGeneratorMetabo_decoy_generation_input_3.mzML'] in_id_cond|in_id: ['AssayGeneratorMetabo_decoy_generation_input.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_1.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_2.featureXML'] out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 6 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: Da adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_2.mzML AssayGeneratorMetabo_decoy_generation_input_3.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML AssayGeneratorMetabo_decoy_generation_input_1.featureXML AssayGeneratorMetabo_decoy_generation_input_2.featureXML value |