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required parameter

advanced parameter

+PTModelTrains a model for the prediction of proteotypic peptides from a training set.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'PTModel'

in_positive input file with positive examplesinput file*.idXML

in_negative input file with negative examplesinput file*.idXML

out output file: the model in libsvm formatoutput file*.txt

c1 the penalty parameter of the svm

svm_typeC_SVC the type of the svm (NU_SVC or C_SVC)NU_SVC,C_SVC

nu0.5 the nu parameter [0..1] of the svm (for nu-SVR)0:1

kernel_typeOLIGO the kernel type of the svmLINEAR,RBF,POLY,OLIGO

degree1 the degree parameter of the kernel function of the svm (POLY kernel)1:∞

border_length22 length of the POBK1:∞

k_mer_length1 k_mer length of the POBK1:∞

sigma5 sigma of the POBK

max_positive_count1000 quantity of positive samples for training (randomly chosen if smaller than available quantity)1:∞

max_negative_count1000 quantity of positive samples for training (randomly chosen if smaller than available quantity)1:∞

redundantfalse if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be settrue,false

additive_cvfalse if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new valuetrue,false

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++cvParameters for the grid search / cross validation:

skip_cvfalse Has to be set if the cv should be skipped and the model should just be trained with the specified parameters.true,false

number_of_runs10 number of runs for the CV1:∞

number_of_partitions10 number of CV partitions2:∞

degree_start1 starting point of degree1:∞

degree_step_size2 step size point of degree

degree_stop4 stopping point of degree

c_start1 starting point of c

c_step_size100 step size of c

c_stop1000 stopping point of c

nu_start0.1 starting point of nu0:1

nu_step_size1.3 step size of nu

nu_stop0.9 stopping point of nu0:1

sigma_start1 starting point of sigma

sigma_step_size1.3 step size of sigma

sigma_stop15 stopping point of sigma