|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="PTModel" name="PTModel" version="2.0.0">
|
|
|
3 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">PTModel</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>PTModel
|
|
|
11
|
|
|
12 #if $param_in_positive:
|
|
|
13 -in_positive $param_in_positive
|
|
|
14 #end if
|
|
|
15 #if $param_in_negative:
|
|
|
16 -in_negative $param_in_negative
|
|
|
17 #end if
|
|
|
18 #if $param_out:
|
|
|
19 -out $param_out
|
|
|
20 #end if
|
|
|
21 #if $param_c:
|
|
|
22 -c $param_c
|
|
|
23 #end if
|
|
|
24 #if $param_svm_type:
|
|
|
25 -svm_type
|
|
|
26 #if " " in str($param_svm_type):
|
|
|
27 "$param_svm_type"
|
|
|
28 #else
|
|
|
29 $param_svm_type
|
|
|
30 #end if
|
|
|
31 #end if
|
|
|
32 #if $param_nu:
|
|
|
33 -nu $param_nu
|
|
|
34 #end if
|
|
|
35 #if $param_kernel_type:
|
|
|
36 -kernel_type
|
|
|
37 #if " " in str($param_kernel_type):
|
|
|
38 "$param_kernel_type"
|
|
|
39 #else
|
|
|
40 $param_kernel_type
|
|
|
41 #end if
|
|
|
42 #end if
|
|
|
43 #if $param_degree:
|
|
|
44 -degree $param_degree
|
|
|
45 #end if
|
|
|
46 #if $param_border_length:
|
|
|
47 -border_length $param_border_length
|
|
|
48 #end if
|
|
|
49 #if $param_k_mer_length:
|
|
|
50 -k_mer_length $param_k_mer_length
|
|
|
51 #end if
|
|
|
52 #if $param_sigma:
|
|
|
53 -sigma $param_sigma
|
|
|
54 #end if
|
|
|
55 #if $param_max_positive_count:
|
|
|
56 -max_positive_count $param_max_positive_count
|
|
|
57 #end if
|
|
|
58 #if $param_max_negative_count:
|
|
|
59 -max_negative_count $param_max_negative_count
|
|
|
60 #end if
|
|
|
61 #if $param_redundant:
|
|
|
62 -redundant
|
|
|
63 #end if
|
|
|
64 #if $param_additive_cv:
|
|
|
65 -additive_cv
|
|
|
66 #end if
|
|
|
67 -threads \${GALAXY_SLOTS:-24}
|
|
|
68 #if $param_cv_skip_cv:
|
|
|
69 -cv:skip_cv
|
|
|
70 #end if
|
|
|
71 #if $param_cv_number_of_runs:
|
|
|
72 -cv:number_of_runs $param_cv_number_of_runs
|
|
|
73 #end if
|
|
|
74 #if $param_cv_number_of_partitions:
|
|
|
75 -cv:number_of_partitions $param_cv_number_of_partitions
|
|
|
76 #end if
|
|
|
77 #if $param_cv_degree_start:
|
|
|
78 -cv:degree_start $param_cv_degree_start
|
|
|
79 #end if
|
|
|
80 #if $param_cv_degree_step_size:
|
|
|
81 -cv:degree_step_size $param_cv_degree_step_size
|
|
|
82 #end if
|
|
|
83 #if $param_cv_degree_stop:
|
|
|
84 -cv:degree_stop $param_cv_degree_stop
|
|
|
85 #end if
|
|
|
86 #if $param_cv_c_start:
|
|
|
87 -cv:c_start $param_cv_c_start
|
|
|
88 #end if
|
|
|
89 #if $param_cv_c_step_size:
|
|
|
90 -cv:c_step_size $param_cv_c_step_size
|
|
|
91 #end if
|
|
|
92 #if $param_cv_c_stop:
|
|
|
93 -cv:c_stop $param_cv_c_stop
|
|
|
94 #end if
|
|
|
95 #if $param_cv_nu_start:
|
|
|
96 -cv:nu_start $param_cv_nu_start
|
|
|
97 #end if
|
|
|
98 #if $param_cv_nu_step_size:
|
|
|
99 -cv:nu_step_size $param_cv_nu_step_size
|
|
|
100 #end if
|
|
|
101 #if $param_cv_nu_stop:
|
|
|
102 -cv:nu_stop $param_cv_nu_stop
|
|
|
103 #end if
|
|
|
104 #if $param_cv_sigma_start:
|
|
|
105 -cv:sigma_start $param_cv_sigma_start
|
|
|
106 #end if
|
|
|
107 #if $param_cv_sigma_step_size:
|
|
|
108 -cv:sigma_step_size $param_cv_sigma_step_size
|
|
|
109 #end if
|
|
|
110 #if $param_cv_sigma_stop:
|
|
|
111 -cv:sigma_stop $param_cv_sigma_stop
|
|
|
112 #end if
|
|
|
113 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
114 #if $adv_opts.param_force:
|
|
|
115 -force
|
|
|
116 #end if
|
|
|
117 #end if
|
|
|
118 </command>
|
|
|
119 <inputs>
|
|
|
120 <param name="param_in_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/>
|
|
|
121 <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/>
|
|
|
122 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
|
|
|
123 <param name="param_svm_type" type="select" optional="True" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) ">
|
|
|
124 <option value="NU_SVC">NU_SVC</option>
|
|
|
125 <option value="C_SVC">C_SVC</option>
|
|
|
126 </param>
|
|
|
127 <param name="param_nu" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help="(-nu) "/>
|
|
|
128 <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
|
|
|
129 <option value="LINEAR">LINEAR</option>
|
|
|
130 <option value="RBF">RBF</option>
|
|
|
131 <option value="POLY">POLY</option>
|
|
|
132 <option value="OLIGO">OLIGO</option>
|
|
|
133 </param>
|
|
|
134 <param name="param_degree" type="integer" min="1" optional="True" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help="(-degree) "/>
|
|
|
135 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
|
|
|
136 <param name="param_k_mer_length" type="integer" min="1" optional="True" value="1" label="k_mer length of the POBK" help="(-k_mer_length) "/>
|
|
|
137 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
|
|
|
138 <param name="param_max_positive_count" type="integer" min="1" optional="True" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help="(-max_positive_count) "/>
|
|
|
139 <param name="param_max_negative_count" type="integer" min="1" optional="True" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help="(-max_negative_count) "/>
|
|
|
140 <param name="param_redundant" type="boolean" truevalue="-redundant" falsevalue="" checked="false" optional="True" label="if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set" help="(-redundant) "/>
|
|
|
141 <param name="param_additive_cv" type="boolean" truevalue="-additive_cv" falsevalue="" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value" help="(-additive_cv) "/>
|
|
|
142 <param name="param_cv_skip_cv" type="boolean" truevalue="-cv:skip_cv" falsevalue="" checked="false" optional="True" label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" help="(-skip_cv) "/>
|
|
|
143 <param name="param_cv_number_of_runs" type="integer" min="1" optional="True" value="10" label="number of runs for the CV" help="(-number_of_runs) "/>
|
|
|
144 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
|
|
|
145 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
|
|
|
146 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
|
|
|
147 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
|
|
|
148 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
|
|
|
149 <param name="param_cv_c_step_size" type="float" value="100.0" label="step size of c" help="(-c_step_size) "/>
|
|
|
150 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
|
|
|
151 <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="starting point of nu" help="(-nu_start) "/>
|
|
|
152 <param name="param_cv_nu_step_size" type="float" value="1.3" label="step size of nu" help="(-nu_step_size) "/>
|
|
|
153 <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.9" label="stopping point of nu" help="(-nu_stop) "/>
|
|
|
154 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
|
|
|
155 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
|
|
|
156 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
|
|
|
157 <expand macro="advanced_options">
|
|
|
158 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
159 </expand>
|
|
|
160 </inputs>
|
|
|
161 <outputs>
|
|
|
162 <data name="param_out" format="txt"/>
|
|
|
163 </outputs>
|
|
|
164 <help>**What it does**
|
|
|
165
|
|
|
166 Trains a model for the prediction of proteotypic peptides from a training set.
|
|
|
167
|
|
|
168
|
|
|
169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help>
|
|
|
170 <expand macro="references"/>
|
|
|
171 </tool>
|
