Repository revision
15:6ccbf9a2072c

Repository 'openms_falsediscoveryrate'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate

FalseDiscoveryRate tool metadata
Miscellaneous
Estimates the false discovery rate on peptide and protein level using decoy searches.
FalseDiscoveryRate
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.8+galaxy0
2.8+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.8+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.5+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.1.0
FalseDiscoveryRate
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.8 package
openms-thirdparty 2.8 package
omssa 2.1.9 package
blast 2.13.0 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: FalseDiscoveryRate_OMSSA.idXML
PSM: True
protein: False
FDR|PSM: 1.0
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: False
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_OMSSA.idXML
value
Test-2 in: FalseDiscoveryRate_OMSSA.idXML
PSM: True
protein: False
FDR|PSM: 1.0
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: False
algorithm|treat_runs_separately: True
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_OMSSA.idXML
value
Test-3 in: FalseDiscoveryRate_OMSSA.idXML
PSM: True
protein: False
FDR|PSM: 1.0
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: True
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_OMSSA.idXML
value
Test-4 in: FalseDiscoveryRate_OMSSA_4.idXML
PSM: True
protein: False
FDR|PSM: 1.0
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: True
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_OMSSA_4.idXML
value
Test-5 in: FalseDiscoveryRate_5_input.idXML
PSM: False
protein: True
FDR|PSM: 1.0
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: False
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: True
algorithm|conservative: True
adv_opts|force: True
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_5_input.idXML
value
Test-6 in: FalseDiscoveryRate_6_input.idXML
PSM: True
protein: False
FDR|PSM: 0.05
FDR|protein: 1.0
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: False
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: False
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_6_input.idXML
value
Test-7 in: FalseDiscoveryRate_7_input.idXML
PSM: False
protein: True
FDR|PSM: 1.0
FDR|protein: 0.3
FDR|cleanup|remove_proteins_without_psms: True
FDR|cleanup|remove_psms_without_proteins: True
FDR|cleanup|remove_spectra_without_psms: True
algorithm|no_qvalues: False
algorithm|use_all_hits: False
algorithm|split_charge_variants: False
algorithm|treat_runs_separately: False
algorithm|add_decoy_peptides: False
algorithm|add_decoy_proteins: False
algorithm|conservative: True
adv_opts|force: True
adv_opts|test: true
OPTIONAL_OUTPUTS: ctd_out_FLAG
name: value
name: value
FalseDiscoveryRate_7_input.idXML
value