| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| 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 (this tool) |
| 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 | 2.6 | 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: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 out_workspace_directory: 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: 0.005 preprocessing|precursor_mz_tolerance_unit: Da preprocessing|precursor_rt_tolerance: 5 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 10 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
| Test-2 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 out_workspace_directory: 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: 0.005 preprocessing|precursor_mz_tolerance_unit: Da preprocessing|precursor_rt_tolerance: 5 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 10 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-3 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 out_workspace_directory: 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: 0.005 preprocessing|precursor_mz_tolerance_unit: Da preprocessing|precursor_rt_tolerance: 5 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 10 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
| Test-4 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 out_workspace_directory: 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: 0.005 preprocessing|precursor_mz_tolerance_unit: Da preprocessing|precursor_rt_tolerance: 5 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 10 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-5 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 out_workspace_directory: 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: 0.005 preprocessing|precursor_mz_tolerance_unit: Da preprocessing|precursor_rt_tolerance: 5 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 10 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-6 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 out_workspace_directory: 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 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 100 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-7 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 out_workspace_directory: 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 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 100 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
| Test-8 |
in: AssayGeneratorMetabo_intsort_input.mzML in_id: AssayGeneratorMetabo_intsort_input.featureXML out_type: tsv fragment_annotation: sirius method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 out_workspace_directory: 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 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 100 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 0.0 adv_opts_cond|max_fragment_mz: 2000.0 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 |
AssayGeneratorMetabo_intsort_input.mzML AssayGeneratorMetabo_intsort_input.featureXML value |
| Test-9 |
in: AssayGeneratorMetabo_input.mzML in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 out_workspace_directory: 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 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False sirius|profile: qtof sirius|candidates: 5 sirius|database: all sirius|noise: 0 sirius|ppm_max: 10 sirius|isotope: both sirius|elements: CHNOP[5]S[8]Cl[1] sirius|compound_timeout: 100 sirius|tree_timeout: 0 sirius|top_n_hits: 10 sirius|auto_charge: False sirius|ion_tree: False sirius|no_recalibration: False sirius|most_intense_ms2: False adv_opts_cond|precursor_recalibration_window: 0.1 adv_opts_cond|precursor_recalibration_window_unit: Da adv_opts_cond|min_fragment_mz: 100.0 adv_opts_cond|max_fragment_mz: 900.0 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 |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |