Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
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 |
Additional information about this tool |
#def quote(s): #set $s = [ _ for _ in $s.split(" ") if _ != "" ] #set $q = False #for $i, $p in enumerate($s): #if $p == "": #continue #end if #if $p.startswith('"'): #set $q = True #end if ## #if p.startswith('-'): ## #set p = "\\" + p ## #elif p.startswith('"-'): ## #set p = "\\" + p[1:] ## #end if #if not $q: #set $s[i] = '"%s"' % p #end if #if $p.endswith('"'): #set $q = False #end if #end for #return " ".join($s) #end def #def oms2gxyext(o) #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'} #return m[o] #end def #def gxy2omsext(g) #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'} #return m[g] #end def #import re ## Preprocessing mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && mkdir database && ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir pin_out && #end if #if $default_params_file: mkdir default_params_file && ln -s '$default_params_file' 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' && #end if ## Main program call set -o pipefail && CometAdapter -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'CometAdapter.ctd' '$args_json' '$hardcoded_json' && CometAdapter -ini CometAdapter.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${gxy2omsext("idxml")}' -database 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -pin_out 'pin_out/output.${gxy2omsext("tabular")}' #end if #if $default_params_file: -default_params_file 'default_params_file/${re.sub("[^\w\-_]", "_", $default_params_file.element_identifier)}.$gxy2omsext($default_params_file.ext)' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("idxml")}' '$out' #if "pin_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'pin_out/output.${gxy2omsext("tabular")}' '$pin_out' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'CometAdapter.ctd' '$ctd_out' #end if
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 |