1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
|
<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="RTModel" description="Trains a model for the retention time prediction of peptides from a training set.">
<ITEM name="version" value="1.8.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'RTModel'">
<ITEM name="in" value="input.idXML" type="string" description="This is the name of the input file (RT prediction). It is assumed that the file type is IdXML. If it is just a textfile having a sequence and the corresponding rt per line, the 'textfile_input' flag has to be set.#br#(valid formats: 'idXML')" tags="input file" />
<ITEM name="textfile_input" value="false" type="string" description="Has to be set if the input file is a textfile containing a sequence with corresponding rt per line (separated by space)." restrictions="true,false" />
<ITEM name="in_positive" value="" type="string" description="input file with positive examples (peptide separation prediction)#br#(valid formats: 'idXML')" tags="input file" />
<ITEM name="in_negative" value="" type="string" description="input file with negative examples (peptide separation prediction)#br#(valid formats: 'idXML')" tags="input file" />
<ITEM name="out" value="svm.model" type="string" description="output file: the model in libsvm format" tags="output file" />
<ITEM name="svm_type" value="NU_SVR" type="string" description="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set#br#to C_SVC for separation prediction)#br#" restrictions="NU_SVR,NU_SVC,EPSILON_SVR,C_SVC" />
<ITEM name="nu" value="0.5" type="float" description="the nu parameter [0..1] of the svm (for nu-SVR)" restrictions="0:1" />
<ITEM name="p" value="0.1" type="float" description="the epsilon parameter of the svm (for epsilon-SVR)" />
<ITEM name="c" value="0.1" type="float" description="the penalty parameter of the svm" />
<ITEM name="kernel_type" value="POLY" type="string" description="the kernel type of the svm" restrictions="LINEAR,RBF,POLY,OLIGO" />
<ITEM name="degree" value="1" type="int" description="the degree parameter of the kernel function of the svm (POLY kernel)#br#" restrictions="1:" />
<ITEM name="border_length" value="22" type="int" description="length of the POBK" restrictions="1:" />
<ITEM name="max_std" value="10" type="float" description="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" restrictions="0:" />
<ITEM name="k_mer_length" value="1" type="int" description="k_mer length of the POBK" restrictions="1:" />
<ITEM name="sigma" value="5" type="float" description="sigma of the POBK" />
<ITEM name="total_gradient_time" value="3000" type="float" description="the time (in seconds) of the gradient (only for RT prediction)" restrictions="1e-005:" />
<ITEM name="first_dim_rt" value="false" type="string" description="if set the model will be built for first_dim_rt" restrictions="true,false" />
<ITEM name="additive_cv" value="false" type="string" description="if the step sizes should be interpreted additively (otherwise the actual value is multiplied#br#with the step size to get the new value" restrictions="true,false" />
<ITEM name="number_of_runs" value="10" type="int" description="number of runs for the CV" restrictions="1:" />
<ITEM name="number_of_partitions" value="10" type="int" description="number of CV partitions" restrictions="2:" />
<ITEM name="degree_start" value="1" type="int" description="starting point of degree" restrictions="1:" />
<ITEM name="degree_step_size" value="2" type="int" description="step size point of degree" />
<ITEM name="degree_stop" value="4" type="int" description="stopping point of degree" />
<ITEM name="p_start" value="1" type="float" description="starting point of p" />
<ITEM name="p_step_size" value="10" type="float" description="step size point of p" />
<ITEM name="p_stop" value="1000" type="float" description="stopping point of p" />
<ITEM name="c_start" value="1" type="float" description="starting point of c" />
<ITEM name="c_step_size" value="10" type="float" description="step size of c" />
<ITEM name="c_stop" value="1000" type="float" description="stopping point of c" />
<ITEM name="nu_start" value="0.3" type="float" description="starting point of nu" restrictions="0:1" />
<ITEM name="nu_step_size" value="1.2" type="float" description="step size of nu" />
<ITEM name="nu_stop" value="0.7" type="float" description="stopping point of nu" restrictions="0:1" />
<ITEM name="sigma_start" value="1" type="float" description="starting point of sigma" />
<ITEM name="sigma_step_size" value="1.3" type="float" description="step size of sigma" />
<ITEM name="sigma_stop" value="15" type="float" description="stopping point of sigma" />
<ITEM name="skip_cv" value="true" type="string" description="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters." restrictions="true,false" />
<ITEM name="log" value="TOPP.log" type="string" description="Location of the log file" tags="advanced" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for software testing only)" tags="advanced" restrictions="true,false" />
</NODE>
</NODE>
</PARAMETERS>
|
