| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.8+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.3.0 |
| CometAdapter |
| 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: spectra_comet.mzML database: proteins.fasta precursor_mass_tolerance: 3.0 precursor_error_units: ppm isotope_error: off fragment_mass_tolerance: 0.50025 fragment_error_units: Da fragment_bin_offset: 0.25 instrument: high_res enzyme: Trypsin num_enzyme_termini: fully missed_cleavages: 1 min_peptide_length: 5 max_peptide_length: 63 num_hits: 5 precursor_charge: 0:0 override_charge: keep any known ms_level: 2 activation_method: ALL max_fragment_charge: 3 clip_nterm_methionine: False fixed_modifications: None variable_modifications: None binary_modifications: reindex: True PeptideIndexing|decoy_string: PeptideIndexing|decoy_string_position: prefix PeptideIndexing|missing_decoy_action: warn PeptideIndexing|write_protein_sequence: False PeptideIndexing|write_protein_description: False PeptideIndexing|keep_unreferenced_proteins: False PeptideIndexing|unmatched_action: error PeptideIndexing|aaa_max: 3 PeptideIndexing|mismatches_max: 0 PeptideIndexing|IL_equivalent: False PeptideIndexing|enzyme|name: auto PeptideIndexing|enzyme|specificity: auto adv_opts|use_A_ions: False adv_opts|use_B_ions: True adv_opts|use_C_ions: False adv_opts|use_X_ions: False adv_opts|use_Y_ions: True adv_opts|use_Z_ions: False adv_opts|use_NL_ions: False adv_opts|second_enzyme: None adv_opts|digest_mass_range: 600:5000 adv_opts|max_precursor_charge: 5 adv_opts|spectrum_batch_size: 1000 adv_opts|mass_offsets: 0.0 adv_opts|minimum_peaks: 10 adv_opts|minimum_intensity: 0.0 adv_opts|remove_precursor_peak: no adv_opts|remove_precursor_tolerance: 1.5 adv_opts|clear_mz_range: 0:0 adv_opts|max_variable_mods_in_peptide: 5 adv_opts|require_variable_mod: False adv_opts|force: True adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'pin_out_FLAG'] |
name: value name: value name: value |
spectra_comet.mzML proteins.fasta value |
| Test-2 |
in: CometAdapter_2_prepared.mzML database: CometAdapter_2_in.fasta precursor_mass_tolerance: 3.0 precursor_error_units: Da isotope_error: off fragment_mass_tolerance: 0.50025 fragment_error_units: Da fragment_bin_offset: 0.25 instrument: high_res enzyme: Trypsin num_enzyme_termini: fully missed_cleavages: 1 min_peptide_length: 5 max_peptide_length: 63 num_hits: 5 precursor_charge: 0:0 override_charge: keep any known ms_level: 2 activation_method: ALL max_fragment_charge: 3 clip_nterm_methionine: False fixed_modifications: None variable_modifications: None binary_modifications: reindex: True PeptideIndexing|decoy_string: PeptideIndexing|decoy_string_position: prefix PeptideIndexing|missing_decoy_action: warn PeptideIndexing|write_protein_sequence: False PeptideIndexing|write_protein_description: False PeptideIndexing|keep_unreferenced_proteins: False PeptideIndexing|unmatched_action: error PeptideIndexing|aaa_max: 3 PeptideIndexing|mismatches_max: 0 PeptideIndexing|IL_equivalent: False PeptideIndexing|enzyme|name: auto PeptideIndexing|enzyme|specificity: auto adv_opts|use_A_ions: False adv_opts|use_B_ions: True adv_opts|use_C_ions: False adv_opts|use_X_ions: False adv_opts|use_Y_ions: True adv_opts|use_Z_ions: False adv_opts|use_NL_ions: False adv_opts|second_enzyme: None adv_opts|digest_mass_range: 600:5000 adv_opts|max_precursor_charge: 5 adv_opts|spectrum_batch_size: 1000 adv_opts|mass_offsets: 0.0 adv_opts|minimum_peaks: 10 adv_opts|minimum_intensity: 0.0 adv_opts|remove_precursor_peak: no adv_opts|remove_precursor_tolerance: 1.5 adv_opts|clear_mz_range: 0:0 adv_opts|max_variable_mods_in_peptide: 5 adv_opts|require_variable_mod: False adv_opts|force: True adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'pin_out_FLAG'] |
name: value name: value name: value |
CometAdapter_2_prepared.mzML CometAdapter_2_in.fasta value |
| Test-3 |
in: CometAdapter_3.mzML database: CometAdapter_3.fasta precursor_mass_tolerance: 5.0 precursor_error_units: ppm isotope_error: off fragment_mass_tolerance: 0.01 fragment_error_units: Da fragment_bin_offset: 0.0 instrument: high_res enzyme: Trypsin num_enzyme_termini: fully missed_cleavages: 3 min_peptide_length: 5 max_peptide_length: 63 num_hits: 5 precursor_charge: 0:0 override_charge: keep known search unknown ms_level: 2 activation_method: ALL max_fragment_charge: 3 clip_nterm_methionine: False fixed_modifications: Carbamidomethyl (C) variable_modifications: ['Acetyl (Protein N-term)', 'Carbamidomethyl (N-term)', 'Phospho (S)', 'Phospho (T)', 'Phospho (Y)'] binary_modifications: reindex: True PeptideIndexing|decoy_string: PeptideIndexing|decoy_string_position: prefix PeptideIndexing|missing_decoy_action: warn PeptideIndexing|write_protein_sequence: False PeptideIndexing|write_protein_description: False PeptideIndexing|keep_unreferenced_proteins: False PeptideIndexing|unmatched_action: error PeptideIndexing|aaa_max: 3 PeptideIndexing|mismatches_max: 0 PeptideIndexing|IL_equivalent: False PeptideIndexing|enzyme|name: auto PeptideIndexing|enzyme|specificity: auto adv_opts|use_A_ions: False adv_opts|use_B_ions: True adv_opts|use_C_ions: False adv_opts|use_X_ions: False adv_opts|use_Y_ions: True adv_opts|use_Z_ions: False adv_opts|use_NL_ions: False adv_opts|second_enzyme: None adv_opts|digest_mass_range: 600:5000 adv_opts|max_precursor_charge: 5 adv_opts|spectrum_batch_size: 20000 adv_opts|mass_offsets: 0.0 adv_opts|minimum_peaks: 10 adv_opts|minimum_intensity: 0.0 adv_opts|remove_precursor_peak: no adv_opts|remove_precursor_tolerance: 1.5 adv_opts|clear_mz_range: 0:0 adv_opts|max_variable_mods_in_peptide: 3 adv_opts|require_variable_mod: False adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ['ctd_out_FLAG', 'pin_out_FLAG'] |
name: value name: value name: value |
CometAdapter_3.mzML CometAdapter_3.fasta value |
| Test-4 |
in: examples/FRACTIONS/BSA1_F1.mzML database: examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta precursor_mass_tolerance: 5.0 precursor_error_units: ppm isotope_error: off fragment_mass_tolerance: 0.01 fragment_error_units: Da fragment_bin_offset: 0.0 instrument: high_res enzyme: Trypsin num_enzyme_termini: fully missed_cleavages: 3 min_peptide_length: 5 max_peptide_length: 63 num_hits: 5 precursor_charge: 0:0 override_charge: keep known search unknown ms_level: 2 activation_method: ALL max_fragment_charge: 3 clip_nterm_methionine: False fixed_modifications: Carbamidomethyl (C) variable_modifications: Met-loss (Protein N-term M) binary_modifications: reindex: True PeptideIndexing|decoy_string: PeptideIndexing|decoy_string_position: prefix PeptideIndexing|missing_decoy_action: warn PeptideIndexing|write_protein_sequence: False PeptideIndexing|write_protein_description: False PeptideIndexing|keep_unreferenced_proteins: False PeptideIndexing|unmatched_action: error PeptideIndexing|aaa_max: 3 PeptideIndexing|mismatches_max: 0 PeptideIndexing|IL_equivalent: False PeptideIndexing|enzyme|name: auto PeptideIndexing|enzyme|specificity: auto adv_opts|use_A_ions: False adv_opts|use_B_ions: True adv_opts|use_C_ions: False adv_opts|use_X_ions: False adv_opts|use_Y_ions: True adv_opts|use_Z_ions: False adv_opts|use_NL_ions: False adv_opts|second_enzyme: None adv_opts|digest_mass_range: 600:1200 adv_opts|max_precursor_charge: 5 adv_opts|spectrum_batch_size: 20000 adv_opts|mass_offsets: 0.0 adv_opts|minimum_peaks: 10 adv_opts|minimum_intensity: 0.0 adv_opts|remove_precursor_peak: no adv_opts|remove_precursor_tolerance: 1.5 adv_opts|clear_mz_range: 0:0 adv_opts|max_variable_mods_in_peptide: 3 adv_opts|require_variable_mod: False adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
examples/FRACTIONS/BSA1_F1.mzML examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta value |