| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.5+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.3.0 |
| PercolatorAdapter |
| Requirements (dependencies defined in the <requirements> tag set) |
| 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: PercolatorAdapter_1.idXML out_type: idXML enzyme: trypsin peptide_level_fdrs: False protein_level_fdrs: False osw_level: ms2 score_type: q-value adv_opts_cond|generic_feature_set: False adv_opts_cond|subset_max_train: 0 adv_opts_cond|cpos: 0.0 adv_opts_cond|cneg: 0.0 adv_opts_cond|testFDR: 0.5 adv_opts_cond|trainFDR: 0.5 adv_opts_cond|maxiter: 10 adv_opts_cond|quick_validation: False adv_opts_cond|default_direction: adv_opts_cond|verbose: 2 adv_opts_cond|unitnorm: False adv_opts_cond|test_each_iteration: False adv_opts_cond|override: False adv_opts_cond|seed: 1 adv_opts_cond|doc: 0 adv_opts_cond|klammer: False adv_opts_cond|decoy_pattern: random adv_opts_cond|post_processing_tdc: False adv_opts_cond|train_best_positive: False adv_opts_cond|ipf_max_peakgroup_pep: 0.7 adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5 adv_opts_cond|ipf_min_transition_sn: 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 |
PercolatorAdapter_1.idXML value |
| Test-2 |
in_osw: PercolatorAdapter_2.osw out_type: osw enzyme: trypsin peptide_level_fdrs: False protein_level_fdrs: False osw_level: ms1 score_type: q-value adv_opts_cond|generic_feature_set: False adv_opts_cond|subset_max_train: 0 adv_opts_cond|cpos: 0.0 adv_opts_cond|cneg: 0.0 adv_opts_cond|testFDR: 0.01 adv_opts_cond|trainFDR: 0.01 adv_opts_cond|maxiter: 10 adv_opts_cond|quick_validation: False adv_opts_cond|default_direction: adv_opts_cond|verbose: 2 adv_opts_cond|unitnorm: False adv_opts_cond|test_each_iteration: False adv_opts_cond|override: False adv_opts_cond|seed: 1 adv_opts_cond|doc: 0 adv_opts_cond|klammer: False adv_opts_cond|decoy_pattern: random adv_opts_cond|post_processing_tdc: False adv_opts_cond|train_best_positive: False adv_opts_cond|ipf_max_peakgroup_pep: 0.7 adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5 adv_opts_cond|ipf_min_transition_sn: 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 |
PercolatorAdapter_2.osw value |
| Test-3 |
in_osw: PercolatorAdapter_2_out1.osw out_type: osw enzyme: trypsin peptide_level_fdrs: False protein_level_fdrs: False osw_level: ms2 score_type: q-value adv_opts_cond|generic_feature_set: False adv_opts_cond|subset_max_train: 0 adv_opts_cond|cpos: 0.0 adv_opts_cond|cneg: 0.0 adv_opts_cond|testFDR: 0.01 adv_opts_cond|trainFDR: 0.01 adv_opts_cond|maxiter: 10 adv_opts_cond|quick_validation: False adv_opts_cond|default_direction: adv_opts_cond|verbose: 2 adv_opts_cond|unitnorm: False adv_opts_cond|test_each_iteration: False adv_opts_cond|override: False adv_opts_cond|seed: 1 adv_opts_cond|doc: 0 adv_opts_cond|klammer: False adv_opts_cond|decoy_pattern: random adv_opts_cond|post_processing_tdc: False adv_opts_cond|train_best_positive: False adv_opts_cond|ipf_max_peakgroup_pep: 0.7 adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5 adv_opts_cond|ipf_min_transition_sn: 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 |
PercolatorAdapter_2_out1.osw value |
| Test-4 |
in_osw: PercolatorAdapter_3_out1.osw out_type: osw enzyme: trypsin peptide_level_fdrs: False protein_level_fdrs: False osw_level: transition score_type: q-value adv_opts_cond|generic_feature_set: False adv_opts_cond|subset_max_train: 0 adv_opts_cond|cpos: 0.0 adv_opts_cond|cneg: 0.0 adv_opts_cond|testFDR: 0.01 adv_opts_cond|trainFDR: 0.01 adv_opts_cond|maxiter: 10 adv_opts_cond|quick_validation: False adv_opts_cond|default_direction: adv_opts_cond|verbose: 2 adv_opts_cond|unitnorm: False adv_opts_cond|test_each_iteration: False adv_opts_cond|override: False adv_opts_cond|seed: 1 adv_opts_cond|doc: 0 adv_opts_cond|klammer: False adv_opts_cond|decoy_pattern: random adv_opts_cond|post_processing_tdc: False adv_opts_cond|train_best_positive: False adv_opts_cond|ipf_max_peakgroup_pep: 0.7 adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5 adv_opts_cond|ipf_min_transition_sn: 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 |
PercolatorAdapter_3_out1.osw value |
| Test-5 |
in: PercolatorAdapter_1.idXML out_type: idXML enzyme: trypsin peptide_level_fdrs: False protein_level_fdrs: False osw_level: ms2 score_type: q-value adv_opts_cond|generic_feature_set: False adv_opts_cond|subset_max_train: 0 adv_opts_cond|cpos: 0.0 adv_opts_cond|cneg: 0.0 adv_opts_cond|testFDR: 0.5 adv_opts_cond|trainFDR: 0.5 adv_opts_cond|maxiter: 10 adv_opts_cond|quick_validation: False adv_opts_cond|default_direction: adv_opts_cond|verbose: 2 adv_opts_cond|unitnorm: False adv_opts_cond|test_each_iteration: False adv_opts_cond|override: False adv_opts_cond|seed: 1 adv_opts_cond|doc: 0 adv_opts_cond|klammer: False adv_opts_cond|decoy_pattern: random adv_opts_cond|post_processing_tdc: False adv_opts_cond|train_best_positive: False adv_opts_cond|ipf_max_peakgroup_pep: 0.7 adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5 adv_opts_cond|ipf_min_transition_sn: 0.0 adv_opts_cond|force: False adv_opts_cond|test: true adv_opts_cond|adv_opts_selector: advanced OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'out_pin_FLAG'] |
name: value name: value name: value |
PercolatorAdapter_1.idXML value |