Repository revision
9:de3eec8c9a17

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

RTModel tool metadata
Miscellaneous
RTModel
Trains a model for the retention time prediction of peptides from a training set.
RTModel
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rtmodel/RTModel/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_rtmodel/RTModel/2.6+galaxy0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rtmodel/RTModel/2.5+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rtmodel/RTModel/2.3.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rtmodel/RTModel/2.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_rtmodel/RTModel/2.1.0
RTModel
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: RTModel_1_input.idXML
svm_type: NU_SVR
nu: 0.5
p: 0.1
c: 0.1
kernel_type: POLY
degree: 1
border_length: 22
max_std: 10.0
k_mer_length: 1
sigma: 5.0
total_gradient_time: 3000.0
first_dim_rt: False
additive_cv: False
cv|skip_cv: True
cv|number_of_runs: 10
cv|number_of_partitions: 10
cv|degree_start: 1
cv|degree_step_size: 2
cv|degree_stop: 4
cv|p_start: 1.0
cv|p_step_size: 10.0
cv|p_stop: 1000.0
cv|c_start: 1.0
cv|c_step_size: 10.0
cv|c_stop: 1000.0
cv|nu_start: 0.3
cv|nu_step_size: 1.2
cv|nu_stop: 0.7
cv|sigma_start: 1.0
cv|sigma_step_size: 1.3
cv|sigma_stop: 15.0
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
RTModel_1_input.idXML
value
Test-2 in_positive: RTModel_2_input_positive.idXML
in_negative: RTModel_2_input_negative.idXML
svm_type: NU_SVR
nu: 0.5
p: 0.1
c: 0.5
kernel_type: OLIGO
degree: 1
border_length: 22
max_std: 10.0
k_mer_length: 1
sigma: 5.0
total_gradient_time: 1.0
first_dim_rt: False
additive_cv: False
cv|skip_cv: True
cv|number_of_runs: 10
cv|number_of_partitions: 10
cv|degree_start: 1
cv|degree_step_size: 2
cv|degree_stop: 4
cv|p_start: 1.0
cv|p_step_size: 10.0
cv|p_stop: 1000.0
cv|c_start: 1.0
cv|c_step_size: 10.0
cv|c_stop: 1000.0
cv|nu_start: 0.3
cv|nu_step_size: 1.2
cv|nu_stop: 0.7
cv|sigma_start: 1.0
cv|sigma_step_size: 1.3
cv|sigma_stop: 15.0
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
RTModel_2_input_positive.idXML
RTModel_2_input_negative.idXML
value
Test-3 in: RTModel_3_input.idXML
svm_type: NU_SVR
nu: 0.5
p: 0.1
c: 0.001953125
kernel_type: OLIGO
degree: 1
border_length: 22
max_std: 10.0
k_mer_length: 1
sigma: 1.0
total_gradient_time: 1.0
first_dim_rt: False
additive_cv: False
cv|skip_cv: False
cv|number_of_runs: 1
cv|number_of_partitions: 5
cv|degree_start: 1
cv|degree_step_size: 2
cv|degree_stop: 4
cv|p_start: 1.0
cv|p_step_size: 10.0
cv|p_stop: 1000.0
cv|c_start: 0.001953125
cv|c_step_size: 2.0
cv|c_stop: 0.001953125
cv|nu_start: 0.4
cv|nu_step_size: 1.2
cv|nu_stop: 0.4
cv|sigma_start: 5.0
cv|sigma_step_size: 1.221055
cv|sigma_stop: 5.0
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
RTModel_3_input.idXML
value
Test-4 in: RTModel_4_input.txt
svm_type: NU_SVR
nu: 0.5
p: 0.1
c: 0.001953125
kernel_type: OLIGO
degree: 1
border_length: 22
max_std: 10.0
k_mer_length: 1
sigma: 1.0
total_gradient_time: 1.0
first_dim_rt: False
additive_cv: False
cv|skip_cv: False
cv|number_of_runs: 1
cv|number_of_partitions: 5
cv|degree_start: 1
cv|degree_step_size: 2
cv|degree_stop: 4
cv|p_start: 1.0
cv|p_step_size: 10.0
cv|p_stop: 1000.0
cv|c_start: 0.001953125
cv|c_step_size: 2.0
cv|c_stop: 0.001953125
cv|nu_start: 0.4
cv|nu_step_size: 1.2
cv|nu_stop: 0.4
cv|sigma_start: 5.0
cv|sigma_step_size: 1.221055
cv|sigma_stop: 5.0
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
RTModel_4_input.txt
value