Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/3.1+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.8+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.5+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.2.0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.1.0 |
IDFileConverter |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
openms | 3.1 | package |
openms-thirdparty | 3.1 | package |
blast | 2.14.1 | package |
ctdopts | 1.5 | 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': 'xsd', 'zip': 'zip'} #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', 'xsd': 'xsd', 'zip': 'zip'} #return m[g] #end def #import re ## Preprocessing mkdir in && cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $mz_file: mkdir mz_file && cp '$mz_file' 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' && #end if ## Main program call set -o pipefail && IDFileConverter -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'IDFileConverter.ctd' '$args_json' '$hardcoded_json' && IDFileConverter -ini IDFileConverter.ctd -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' -out 'out/output.${out_type}' #if $mz_file: -mz_file 'mz_file/${re.sub("[^\w\-_]", "_", $mz_file.element_identifier)}.$gxy2omsext($mz_file.ext)' #end if ## Postprocessing && mv 'out/output.${out_type}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'IDFileConverter.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in: IDFileConverter_1_input1.mascotXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_1_input1.mascotXML IDFileConverter_1_input2.mzML value |
Test-2 |
in: PepXMLFile_test.pepxml out_type: idXML mz_file: PepXMLFile_test.mzML mz_name: PepXMLFile_test peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
PepXMLFile_test.pepxml PepXMLFile_test.mzML value |
Test-3 |
in: IDFileConverter_3_input.protXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_3_input.protXML value |
Test-4 |
in: IDFileConverter_1_input1.mascotXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: scan=(?<SCAN>\d+) adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_1_input1.mascotXML IDFileConverter_1_input2.mzML value |
Test-5 |
in: IDFileConverter_6_input1.pepXML out_type: idXML mz_file: IDFileConverter_1_input2.mzML mz_name: F025589.dat.mzML peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_6_input1.pepXML IDFileConverter_1_input2.mzML value |
Test-6 |
in: IDFileConverter_7_input1.xml out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_7_input1.xml value |
Test-7 |
in: IDFileConverter_8_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_8_input.mzid value |
Test-8 |
in: IDFileConverter_9_input.idXML out_type: mzid mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_9_input.idXML value |
Test-9 |
in: IDFileConverter_10_input.pepXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_10_input.pepXML value |
Test-10 |
in: IDFileConverter_11_input.tsv out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_11_input.tsv value |
Test-11 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_12_input.psms value |
Test-12 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: PEP fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_12_input.psms value |
Test-13 |
in: IDFileConverter_12_input.psms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: score fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_12_input.psms value |
Test-14 |
in: MSGFPlusAdapter_1_out.mzid out_type: idXML mz_file: spectra.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
MSGFPlusAdapter_1_out.mzid spectra.mzML value |
Test-15 |
in: IDFileConverter_16_input.pepXML out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_16_input.pepXML value |
Test-16 |
in: IDFileConverter_17_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_17_input.idXML value |
Test-17 |
in: IDFileConverter_18_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_18_input.idXML value |
Test-18 |
in: IDFileConverter_19_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_19_input.idXML value |
Test-19 |
in: IDFileConverter_20_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_20_input.idXML value |
Test-20 |
in: IDFileConverter_21_input.idXML out_type: idXML mz_file: IDMapper_4_input.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_21_input.idXML IDMapper_4_input.mzML value |
Test-21 |
in: MSGFPlusAdapter_1_out.mzid out_type: idXML mz_file: spectra.mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.01 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
MSGFPlusAdapter_1_out.mzid spectra.mzML value |
Test-22 |
in: IDFileConverter_23_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_23_input.mzid value |
Test-23 |
in: IDFileConverter_24_input.pep.xml out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_24_input.pep.xml value |
Test-24 |
in: IDFileConverter_25_input.idXML out_type: pepXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_25_input.idXML value |
Test-25 |
in: IDFileConverter_26_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_26_input.mzid value |
Test-26 |
in: IDFileConverter_27_input.idXML out_type: fasta mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_27_input.idXML value |
Test-27 |
in: IDFileConverter_27_input.idXML out_type: fasta mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: -1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_27_input.idXML value |
Test-28 |
in: IDFileConverter_27_input.idXML out_type: fasta mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: True adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_27_input.idXML value |
Test-29 |
in: IDFileConverter_27_input.idXML out_type: fasta mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: True adv_opts|number_of_hits: 2 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_27_input.idXML value |
Test-30 |
in: IDFileConverter_31_input.mzid out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_31_input.mzid value |
Test-31 |
in: IDFileConverter_32_input.FASTA out_type: mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_32_input.FASTA value |
Test-32 |
in: IDFileConverter_32_input.FASTA out_type: mzML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 1 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 3 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_32_input.FASTA value |
Test-33 |
in: IDFileConverter_34_input.idXML out_type: oms mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_34_input.idXML value |
Test-34 |
in: IDFileConverter_34_output1.oms out_type: idXML mz_name: peptideprophet_analyzed: False score_type: qvalue fasta_to_mzml|isotope_model: none fasta_to_mzml|max_isotope: 2 fasta_to_mzml|max_isotope_probability: 0.05 fasta_to_mzml|add_metainfo: False fasta_to_mzml|add_losses: False fasta_to_mzml|sort_by_position: True fasta_to_mzml|add_precursor_peaks: False fasta_to_mzml|add_all_precursor_charges: False fasta_to_mzml|add_abundant_immonium_ions: False fasta_to_mzml|add_first_prefix_ion: False fasta_to_mzml|add_y_ions: True fasta_to_mzml|add_b_ions: True fasta_to_mzml|add_a_ions: False fasta_to_mzml|add_c_ions: False fasta_to_mzml|add_x_ions: False fasta_to_mzml|add_z_ions: False fasta_to_mzml|y_intensity: 1.0 fasta_to_mzml|b_intensity: 1.0 fasta_to_mzml|a_intensity: 1.0 fasta_to_mzml|c_intensity: 1.0 fasta_to_mzml|x_intensity: 1.0 fasta_to_mzml|z_intensity: 1.0 fasta_to_mzml|relative_loss_intensity: 0.1 fasta_to_mzml|precursor_intensity: 1.0 fasta_to_mzml|precursor_H2O_intensity: 1.0 fasta_to_mzml|precursor_NH3_intensity: 1.0 fasta_to_mzml|enzyme: Trypsin fasta_to_mzml|missed_cleavages: 0 fasta_to_mzml|min_charge: 1 fasta_to_mzml|max_charge: 1 fasta_to_mzml|precursor_charge: 0 adv_opts|ignore_proteins_per_peptide: False adv_opts|scan_regex: adv_opts|no_spectra_data_override: False adv_opts|no_spectra_references_override: False adv_opts|add_ionmatch_annotation: 0.0 adv_opts|concatenate_peptides: False adv_opts|number_of_hits: 1 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
IDFileConverter_34_output1.oms value |