| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.3.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.2.0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursorionselector/PrecursorIonSelector/2.1.0 |
| PrecursorIonSelector |
| 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: PrecursorIonSelector_features.featureXML ids: PrecursorIonSelector_ids.idXML num_precursors: 1 load_preprocessing: False store_preprocessing: False simulation: True db_path: PrecursorIonSelector_db.fasta fixed_modifications: algorithm|type: IPS algorithm|max_iteration: 10 algorithm|rt_bin_capacity: 10 algorithm|step_size: 1 algorithm|peptide_min_prob: 0.2 algorithm|sequential_spectrum_order: False algorithm|MIPFormulation|thresholds|min_protein_probability: 0.2 algorithm|MIPFormulation|thresholds|min_protein_id_probability: 0.95 algorithm|MIPFormulation|thresholds|min_pt_weight: 0.5 algorithm|MIPFormulation|thresholds|min_mz: 500.0 algorithm|MIPFormulation|thresholds|max_mz: 5000.0 algorithm|MIPFormulation|thresholds|min_pred_pep_prob: 0.5 algorithm|MIPFormulation|thresholds|min_rt_weight: 0.5 algorithm|MIPFormulation|thresholds|use_peptide_rule: True algorithm|MIPFormulation|thresholds|min_peptide_ids: 2 algorithm|MIPFormulation|thresholds|min_peptide_probability: 0.95 algorithm|MIPFormulation|combined_ilp|k1: 0.2 algorithm|MIPFormulation|combined_ilp|k2: 0.2 algorithm|MIPFormulation|combined_ilp|k3: 0.4 algorithm|MIPFormulation|combined_ilp|scale_matching_probs: True algorithm|MIPFormulation|feature_based|no_intensity_normalization: False algorithm|MIPFormulation|feature_based|max_number_precursors_per_feature: 1 algorithm|Preprocessing|precursor_mass_tolerance: 0.9 algorithm|Preprocessing|precursor_mass_tolerance_unit: Da algorithm|Preprocessing|preprocessed_db_path: algorithm|Preprocessing|preprocessed_db_pred_rt_path: algorithm|Preprocessing|preprocessed_db_pred_dt_path: algorithm|Preprocessing|max_peptides_per_run: 100000 algorithm|Preprocessing|missed_cleavages: 1 algorithm|Preprocessing|taxonomy: algorithm|Preprocessing|store_peptide_sequences: false algorithm|Preprocessing|rt_settings|min_rt: 960.0 algorithm|Preprocessing|rt_settings|max_rt: 3840.0 algorithm|Preprocessing|rt_settings|rt_step_size: 30.0 algorithm|Preprocessing|rt_settings|gauss_mean: -1.0 algorithm|Preprocessing|rt_settings|gauss_sigma: 3.0 adv_opts_cond|solver: GLPK adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'sim_results_FLAG'] |
name: value name: value |
PrecursorIonSelector_features.featureXML PrecursorIonSelector_ids.idXML PrecursorIonSelector_db.fasta value |
| Test-2 |
in: PrecursorIonSelector_features.featureXML ids: PrecursorIonSelector_ids.idXML num_precursors: 1 load_preprocessing: False store_preprocessing: False simulation: False db_path: PrecursorIonSelector_db.fasta fixed_modifications: algorithm|type: IPS algorithm|max_iteration: 10 algorithm|rt_bin_capacity: 10 algorithm|step_size: 1 algorithm|peptide_min_prob: 0.2 algorithm|sequential_spectrum_order: False algorithm|MIPFormulation|thresholds|min_protein_probability: 0.2 algorithm|MIPFormulation|thresholds|min_protein_id_probability: 0.95 algorithm|MIPFormulation|thresholds|min_pt_weight: 0.5 algorithm|MIPFormulation|thresholds|min_mz: 500.0 algorithm|MIPFormulation|thresholds|max_mz: 5000.0 algorithm|MIPFormulation|thresholds|min_pred_pep_prob: 0.5 algorithm|MIPFormulation|thresholds|min_rt_weight: 0.5 algorithm|MIPFormulation|thresholds|use_peptide_rule: True algorithm|MIPFormulation|thresholds|min_peptide_ids: 2 algorithm|MIPFormulation|thresholds|min_peptide_probability: 0.95 algorithm|MIPFormulation|combined_ilp|k1: 0.2 algorithm|MIPFormulation|combined_ilp|k2: 0.2 algorithm|MIPFormulation|combined_ilp|k3: 0.4 algorithm|MIPFormulation|combined_ilp|scale_matching_probs: True algorithm|MIPFormulation|feature_based|no_intensity_normalization: False algorithm|MIPFormulation|feature_based|max_number_precursors_per_feature: 1 algorithm|Preprocessing|precursor_mass_tolerance: 0.9 algorithm|Preprocessing|precursor_mass_tolerance_unit: Da algorithm|Preprocessing|preprocessed_db_path: algorithm|Preprocessing|preprocessed_db_pred_rt_path: algorithm|Preprocessing|preprocessed_db_pred_dt_path: algorithm|Preprocessing|max_peptides_per_run: 100000 algorithm|Preprocessing|missed_cleavages: 1 algorithm|Preprocessing|taxonomy: algorithm|Preprocessing|store_peptide_sequences: false algorithm|Preprocessing|rt_settings|min_rt: 960.0 algorithm|Preprocessing|rt_settings|max_rt: 3840.0 algorithm|Preprocessing|rt_settings|rt_step_size: 30.0 algorithm|Preprocessing|rt_settings|gauss_mean: -1.0 algorithm|Preprocessing|rt_settings|gauss_sigma: 3.0 adv_opts_cond|solver: GLPK adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_FLAG'] |
name: value name: value |
PrecursorIonSelector_features.featureXML PrecursorIonSelector_ids.idXML PrecursorIonSelector_db.fasta value |