Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.8+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.6+galaxy1 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.6+galaxy0 |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_assaygeneratormetabo/AssayGeneratorMetabo/2.5+galaxy0 |
AssayGeneratorMetabo |
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 #if $sirius_executable: mkdir sirius_executable && ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' && #end if mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir in_id_cond.in_id && #if $in_id_cond.in_id_select == "no" mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} && ${' '.join(["ln -s '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])} #else ln -s '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' && #end if mkdir out && ## Main program call set -o pipefail && AssayGeneratorMetabo -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' 'AssayGeneratorMetabo.ctd' '$args_json' '$hardcoded_json' && AssayGeneratorMetabo -ini AssayGeneratorMetabo.ctd #if $sirius_executable: -sirius_executable 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' #end if -in #if $in_cond.in_select == "no" ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' #end if -in_id #if $in_id_cond.in_id_select == "no" ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])} #else 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' #end if -out 'out/output.${out_type}' ## Postprocessing && mv 'out/output.${out_type}' '$out' #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv 'AssayGeneratorMetabo.ctd' '$ctd_out' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
Test-2 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-3 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ffm_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ffm_input.featureXML value |
Test-4 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-5 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: none ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: consensus_spectrum use_exact_mass: False exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 5.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: False preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-6 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-7 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: True min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: ALL fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-8 |
in_cond|in: AssayGeneratorMetabo_intsort_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_intsort_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_intsort_input.mzML AssayGeneratorMetabo_intsort_input.featureXML value |
Test-9 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: False decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 2 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-10 |
in_cond|in: AssayGeneratorMetabo_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_ams_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 3 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_input.mzML AssayGeneratorMetabo_ams_input.featureXML value |
Test-11 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: original method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
Test-12 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: resolve_overlap method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
Test-13 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: add_shift method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
Test-14 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML value |
Test-15 |
in_cond|in: AssayGeneratorMetabo_decoy_generation_input.mzML in_id_cond|in_id: AssayGeneratorMetabo_decoy_generation_input_multids.featureXML out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 3 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: ppm adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 100.0 adv_opts|max_fragment_mz: 900.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_multids.featureXML value |
Test-16 |
in_cond|in: ['AssayGeneratorMetabo_decoy_generation_input.mzML', 'AssayGeneratorMetabo_decoy_generation_input_2.mzML', 'AssayGeneratorMetabo_decoy_generation_input_3.mzML'] in_id_cond|in_id: ['AssayGeneratorMetabo_decoy_generation_input.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_1.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_2.featureXML'] out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.8 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 6 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: Da adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_2.mzML AssayGeneratorMetabo_decoy_generation_input_3.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML AssayGeneratorMetabo_decoy_generation_input_1.featureXML AssayGeneratorMetabo_decoy_generation_input_2.featureXML value |
Test-17 |
in_cond|in: ['AssayGeneratorMetabo_decoy_generation_input.mzML', 'AssayGeneratorMetabo_decoy_generation_input_2.mzML', 'AssayGeneratorMetabo_decoy_generation_input_3.mzML'] in_id_cond|in_id: ['AssayGeneratorMetabo_decoy_generation_input.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_1.featureXML', 'AssayGeneratorMetabo_decoy_generation_input_2.featureXML'] out_type: tsv fragment_annotation: sirius ambiguity_resolution_mz_tolerance: 10.0 ambiguity_resolution_rt_tolerance: 10.0 total_occurrence_filter: 0.1 fragment_annotation_score_threshold: 0.8 decoy_generation: True decoy_generation_method: both method: highest_intensity use_exact_mass: True exclude_ms2_precursor: False precursor_mz_distance: 0.0001 consensus_spectrum_precursor_rt_tolerance: 5.0 use_known_unknowns: False min_transitions: 1 max_transitions: 6 cosine_similarity_threshold: 0.98 transition_threshold: 3.0 deisotoping|use_deisotoper: False deisotoping|fragment_tolerance: 1.0 deisotoping|fragment_unit: ppm deisotoping|min_charge: 1 deisotoping|max_charge: 1 deisotoping|min_isopeaks: 2 deisotoping|max_isopeaks: 3 deisotoping|keep_only_deisotoped: False deisotoping|annotate_charge: False preprocessing|filter_by_num_masstraces: 1 preprocessing|precursor_mz_tolerance: 10.0 preprocessing|precursor_mz_tolerance_unit: ppm preprocessing|precursor_rt_tolerance: 5.0 preprocessing|isotope_pattern_iterations: 3 preprocessing|feature_only: True preprocessing|no_masstrace_info_isotope_pattern: False project|processors: 1 project|ignore_formula: False project|q: False sirius|ppm_max: 10.0 sirius|ppm_max_ms2: 10.0 sirius|tree_timeout: 0 sirius|compound_timeout: 100 sirius|no_recalibration: False sirius|profile: qtof sirius|formula: sirius|ions_enforced: sirius|candidates: 5 sirius|candidates_per_ion: -1 sirius|elements_considered: sirius|elements_enforced: sirius|no_isotope_score: False sirius|no_isotope_filter: False sirius|ions_considered: sirius|db: fingerid|candidates: 10 fingerid|db: BIO adv_opts|ambiguity_resolution_mz_tolerance_unit: Da adv_opts|precursor_recalibration_window: 0.01 adv_opts|precursor_recalibration_window_unit: Da adv_opts|min_fragment_mz: 0.0 adv_opts|max_fragment_mz: 2000.0 adv_opts|force: False adv_opts|test: true OPTIONAL_OUTPUTS: ctd_out_FLAG |
name: value name: value |
AssayGeneratorMetabo_decoy_generation_input.mzML AssayGeneratorMetabo_decoy_generation_input_2.mzML AssayGeneratorMetabo_decoy_generation_input_3.mzML AssayGeneratorMetabo_decoy_generation_input.featureXML AssayGeneratorMetabo_decoy_generation_input_1.featureXML AssayGeneratorMetabo_decoy_generation_input_2.featureXML value |