Repository revision
10:965413f29bf5

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

OpenSwathDecoyGenerator tool metadata
Miscellaneous
Generates decoys according to different models for a specific TraML
OpenSwathDecoyGenerator
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0
2.5+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathdecoygenerator/OpenSwathDecoyGenerator/2.1.0
OpenSwathDecoyGenerator
Requirements (dependencies defined in the <requirements> tag set)
name version type
openms 2.5 package
openms-thirdparty 2.5 package
blast 2.9.0 package
openjdk 8.0.192 package
ctdopts 1.4 package
Functional tests
name inputs outputs required files
Test-1 in: OpenSwathDecoyGenerator_input.TraML
out_type: TraML
method: pseudo-reverse
decoy_tag: DECOY_
switchKR: False
adv_opts_cond|min_decoy_fraction: 0.8
adv_opts_cond|aim_decoy_fraction: 1.0
adv_opts_cond|shuffle_max_attempts: 30
adv_opts_cond|shuffle_sequence_identity_threshold: 0.5
adv_opts_cond|shift_precursor_mz_shift: 0.0
adv_opts_cond|shift_product_mz_shift: 20.0
adv_opts_cond|product_mz_threshold: 0.025
adv_opts_cond|allowed_fragment_types: b,y
adv_opts_cond|allowed_fragment_charges: 1,2,3,4
adv_opts_cond|enable_detection_specific_losses: False
adv_opts_cond|enable_detection_unspecific_losses: False
adv_opts_cond|separate: True
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
OpenSwathDecoyGenerator_input.TraML
value
Test-2 in: OpenSwathDecoyGenerator_input_2.TraML
out_type: TraML
method: pseudo-reverse
decoy_tag: DECOY_
switchKR: False
adv_opts_cond|min_decoy_fraction: 0.8
adv_opts_cond|aim_decoy_fraction: 1.0
adv_opts_cond|shuffle_max_attempts: 30
adv_opts_cond|shuffle_sequence_identity_threshold: 0.5
adv_opts_cond|shift_precursor_mz_shift: 0.0
adv_opts_cond|shift_product_mz_shift: 20.0
adv_opts_cond|product_mz_threshold: 0.8
adv_opts_cond|allowed_fragment_types: b,y
adv_opts_cond|allowed_fragment_charges: 1,2,3,4
adv_opts_cond|enable_detection_specific_losses: False
adv_opts_cond|enable_detection_unspecific_losses: False
adv_opts_cond|separate: False
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
OpenSwathDecoyGenerator_input_2.TraML
value
Test-3 in: OpenSwathDecoyGenerator_input_3.TraML
out_type: TraML
method: pseudo-reverse
decoy_tag: DECOY_
switchKR: False
adv_opts_cond|min_decoy_fraction: 0.8
adv_opts_cond|aim_decoy_fraction: 1.0
adv_opts_cond|shuffle_max_attempts: 30
adv_opts_cond|shuffle_sequence_identity_threshold: 0.5
adv_opts_cond|shift_precursor_mz_shift: 0.0
adv_opts_cond|shift_product_mz_shift: 20.0
adv_opts_cond|product_mz_threshold: 0.025
adv_opts_cond|allowed_fragment_types: b,y
adv_opts_cond|allowed_fragment_charges: 1,2,3,4
adv_opts_cond|enable_detection_specific_losses: False
adv_opts_cond|enable_detection_unspecific_losses: False
adv_opts_cond|separate: True
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
OpenSwathDecoyGenerator_input_3.TraML
value
Test-4 in: OpenSwathDecoyGenerator_input_4.tsv
out_type: TraML
method: pseudo-reverse
decoy_tag: DECOY_
switchKR: True
adv_opts_cond|min_decoy_fraction: 0.4
adv_opts_cond|aim_decoy_fraction: 1.0
adv_opts_cond|shuffle_max_attempts: 30
adv_opts_cond|shuffle_sequence_identity_threshold: 0.5
adv_opts_cond|shift_precursor_mz_shift: 0.0
adv_opts_cond|shift_product_mz_shift: 20.0
adv_opts_cond|product_mz_threshold: 0.025
adv_opts_cond|allowed_fragment_types: b,y
adv_opts_cond|allowed_fragment_charges: 1,2,3,4
adv_opts_cond|enable_detection_specific_losses: True
adv_opts_cond|enable_detection_unspecific_losses: True
adv_opts_cond|separate: True
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
OpenSwathDecoyGenerator_input_4.tsv
value