| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_epifany/Epifany/2.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_epifany/Epifany/2.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_epifany/Epifany/2.5+galaxy0 |
| Epifany |
| 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: FidoAdapter_1_input.idXML out_type: idXML protein_fdr: False greedy_group_resolution: none max_psms_extreme_probability: 1.0 algorithm|psm_probability_cutoff: 0.001 algorithm|top_PSMs: 1 algorithm|keep_best_PSM_only: True algorithm|update_PSM_probabilities: True algorithm|user_defined_priors: False algorithm|annotate_group_probabilities: True algorithm|use_ids_outside_features: False algorithm|model_parameters|prot_prior: 0.7 algorithm|model_parameters|pep_emission: 0.1 algorithm|model_parameters|pep_spurious_emission: 0.001 algorithm|model_parameters|pep_prior: 0.1 algorithm|model_parameters|regularize: False algorithm|model_parameters|extended_model: False algorithm|loopy_belief_propagation|scheduling_type: priority algorithm|loopy_belief_propagation|convergence_threshold: 1e-05 algorithm|loopy_belief_propagation|dampening_lambda: 0.001 algorithm|loopy_belief_propagation|max_nr_iterations: 2147483647 algorithm|loopy_belief_propagation|p_norm_inference: 1.0 algorithm|param_optimize|aucweight: 0.3 algorithm|param_optimize|conservative_fdr: True algorithm|param_optimize|regularized_fdr: True adv_opts_cond|conservative_fdr: True adv_opts_cond|min_psms_extreme_probability: 0.0 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 |
FidoAdapter_1_input.idXML value |
| Test-2 |
in: Epifany_2_input.consensusXML out_type: consensusXML protein_fdr: False greedy_group_resolution: none max_psms_extreme_probability: 1.0 algorithm|psm_probability_cutoff: 0.001 algorithm|top_PSMs: 1 algorithm|keep_best_PSM_only: True algorithm|update_PSM_probabilities: True algorithm|user_defined_priors: False algorithm|annotate_group_probabilities: True algorithm|use_ids_outside_features: False algorithm|model_parameters|prot_prior: 0.7 algorithm|model_parameters|pep_emission: 0.1 algorithm|model_parameters|pep_spurious_emission: 0.001 algorithm|model_parameters|pep_prior: 0.1 algorithm|model_parameters|regularize: False algorithm|model_parameters|extended_model: False algorithm|loopy_belief_propagation|scheduling_type: priority algorithm|loopy_belief_propagation|convergence_threshold: 1e-05 algorithm|loopy_belief_propagation|dampening_lambda: 0.001 algorithm|loopy_belief_propagation|max_nr_iterations: 2147483647 algorithm|loopy_belief_propagation|p_norm_inference: 1.0 algorithm|param_optimize|aucweight: 0.3 algorithm|param_optimize|conservative_fdr: True algorithm|param_optimize|regularized_fdr: True adv_opts_cond|conservative_fdr: True adv_opts_cond|min_psms_extreme_probability: 0.0 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 |
Epifany_2_input.consensusXML value |
| Test-3 |
in: Epifany_2_input.consensusXML out_type: consensusXML protein_fdr: False greedy_group_resolution: none max_psms_extreme_probability: 1.0 algorithm|psm_probability_cutoff: 0.001 algorithm|top_PSMs: 1 algorithm|keep_best_PSM_only: False algorithm|update_PSM_probabilities: True algorithm|user_defined_priors: False algorithm|annotate_group_probabilities: True algorithm|use_ids_outside_features: False algorithm|model_parameters|prot_prior: 0.7 algorithm|model_parameters|pep_emission: 0.1 algorithm|model_parameters|pep_spurious_emission: 0.001 algorithm|model_parameters|pep_prior: 0.1 algorithm|model_parameters|regularize: False algorithm|model_parameters|extended_model: False algorithm|loopy_belief_propagation|scheduling_type: priority algorithm|loopy_belief_propagation|convergence_threshold: 1e-05 algorithm|loopy_belief_propagation|dampening_lambda: 0.001 algorithm|loopy_belief_propagation|max_nr_iterations: 2147483647 algorithm|loopy_belief_propagation|p_norm_inference: 1.0 algorithm|param_optimize|aucweight: 0.3 algorithm|param_optimize|conservative_fdr: True algorithm|param_optimize|regularized_fdr: True adv_opts_cond|conservative_fdr: True adv_opts_cond|min_psms_extreme_probability: 0.0 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 |
Epifany_2_input.consensusXML value |