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PercolatorAdapter tool metadata

Miscellaneous

Name: PercolatorAdapter

Description: Facilitate input to Percolator and reintegrate.

Id: PercolatorAdapter

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.6+galaxy0

Version: 2.6+galaxy0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.8+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.6+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.5+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/openms_percolatoradapter/PercolatorAdapter/2.3.0

PercolatorAdapter

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

openms

2.6

package

openms-thirdparty

2.6

package

blast

2.9.0

package

ctdopts

1.4

package

Functional tests

name

inputs

outputs

required files

Test-1

in: PercolatorAdapter_1.idXML
out_type: idXML
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms2
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.5
adv_opts_cond|trainFDR: 0.5
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PercolatorAdapter_1.idXML
value

Test-2

in_osw: PercolatorAdapter_2.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms1
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PercolatorAdapter_2.osw
value

Test-3

in_osw: PercolatorAdapter_2_out1.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: ms2
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PercolatorAdapter_2_out1.osw
value

Test-4

in_osw: PercolatorAdapter_3_out1.osw
out_type: osw
enzyme: trypsin
peptide_level_fdrs: False
protein_level_fdrs: False
osw_level: transition
score_type: q-value
adv_opts_cond|generic_feature_set: False
adv_opts_cond|subset_max_train: 0
adv_opts_cond|cpos: 0.0
adv_opts_cond|cneg: 0.0
adv_opts_cond|testFDR: 0.01
adv_opts_cond|trainFDR: 0.01
adv_opts_cond|maxiter: 10
adv_opts_cond|nested_xval_bins: 1
adv_opts_cond|quick_validation: False
adv_opts_cond|static: False
adv_opts_cond|default_direction:
adv_opts_cond|verbose: 2
adv_opts_cond|unitnorm: False
adv_opts_cond|test_each_iteration: False
adv_opts_cond|override: False
adv_opts_cond|seed: 1
adv_opts_cond|doc: 0
adv_opts_cond|klammer: False
adv_opts_cond|decoy_pattern: random
adv_opts_cond|post_processing_tdc: False
adv_opts_cond|train_best_positive: False
adv_opts_cond|ipf_max_peakgroup_pep: 0.7
adv_opts_cond|ipf_max_transition_isotope_overlap: 0.5
adv_opts_cond|ipf_min_transition_sn: 0.0
adv_opts_cond|force: False
adv_opts_cond|test: true
adv_opts_cond|adv_opts_selector: advanced
OPTIONAL_OUTPUTS: ctd_out_FLAG

name: value
name: value

PercolatorAdapter_3_out1.osw
value

Test-5

name: value
name: value
name: value

PercolatorAdapter_1.idXML
value