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comparison RTModel.xml @ 0:3070d71e0e5c draft

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author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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-1:000000000000 0:3070d71e0e5c
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="RTModel" name="RTModel" version="2.0.0">
3 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
4 <macros>
5 <token name="@EXECUTABLE@">RTModel</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>RTModel
11
12 #if $param_in:
13 -in $param_in
14 #end if
15 #if $param_in_positive:
16 -in_positive $param_in_positive
17 #end if
18 #if $param_in_negative:
19 -in_negative $param_in_negative
20 #end if
21 #if $param_out:
22 -out $param_out
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_p:
36 -p $param_p
37 #end if
38 #if $param_c:
39 -c $param_c
40 #end if
41 #if $param_kernel_type:
42 -kernel_type
43 #if " " in str($param_kernel_type):
44 "$param_kernel_type"
45 #else
46 $param_kernel_type
47 #end if
48 #end if
49 #if $param_degree:
50 -degree $param_degree
51 #end if
52 #if $param_border_length:
53 -border_length $param_border_length
54 #end if
55 #if $param_max_std:
56 -max_std $param_max_std
57 #end if
58 #if $param_k_mer_length:
59 -k_mer_length $param_k_mer_length
60 #end if
61 #if $param_sigma:
62 -sigma $param_sigma
63 #end if
64 #if $param_total_gradient_time:
65 -total_gradient_time $param_total_gradient_time
66 #end if
67 #if $param_first_dim_rt:
68 -first_dim_rt
69 #end if
70 #if $param_additive_cv:
71 -additive_cv
72 #end if
73 -threads \${GALAXY_SLOTS:-24}
74 #if $param_cv_skip_cv:
75 -cv:skip_cv
76 #end if
77 #if $param_cv_number_of_runs:
78 -cv:number_of_runs $param_cv_number_of_runs
79 #end if
80 #if $param_cv_number_of_partitions:
81 -cv:number_of_partitions $param_cv_number_of_partitions
82 #end if
83 #if $param_cv_degree_start:
84 -cv:degree_start $param_cv_degree_start
85 #end if
86 #if $param_cv_degree_step_size:
87 -cv:degree_step_size $param_cv_degree_step_size
88 #end if
89 #if $param_cv_degree_stop:
90 -cv:degree_stop $param_cv_degree_stop
91 #end if
92 #if $param_cv_p_start:
93 -cv:p_start $param_cv_p_start
94 #end if
95 #if $param_cv_p_step_size:
96 -cv:p_step_size $param_cv_p_step_size
97 #end if
98 #if $param_cv_p_stop:
99 -cv:p_stop $param_cv_p_stop
100 #end if
101 #if $param_cv_c_start:
102 -cv:c_start $param_cv_c_start
103 #end if
104 #if $param_cv_c_step_size:
105 -cv:c_step_size $param_cv_c_step_size
106 #end if
107 #if $param_cv_c_stop:
108 -cv:c_stop $param_cv_c_stop
109 #end if
110 #if $param_cv_nu_start:
111 -cv:nu_start $param_cv_nu_start
112 #end if
113 #if $param_cv_nu_step_size:
114 -cv:nu_step_size $param_cv_nu_step_size
115 #end if
116 #if $param_cv_nu_stop:
117 -cv:nu_stop $param_cv_nu_stop
118 #end if
119 #if $param_cv_sigma_start:
120 -cv:sigma_start $param_cv_sigma_start
121 #end if
122 #if $param_cv_sigma_step_size:
123 -cv:sigma_step_size $param_cv_sigma_step_size
124 #end if
125 #if $param_cv_sigma_stop:
126 -cv:sigma_stop $param_cv_sigma_stop
127 #end if
128 #if $adv_opts.adv_opts_selector=='advanced':
129 #if $adv_opts.param_force:
130 -force
131 #end if
132 #end if
133 </command>
134 <inputs>
135 <param name="param_in" type="data" format="txt,idxml" optional="True" label="This is the name of the input file (RT prediction)" help="(-in) It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line. &lt;br&gt;"/>
136 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/>
137 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/>
138 <param name="param_svm_type" type="select" optional="True" value="NU_SVR" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set &lt;br&gt;to C_SVC for separation prediction)" help="(-svm_type) ">
139 <option value="NU_SVR">NU_SVR</option>
140 <option value="NU_SVC">NU_SVC</option>
141 <option value="EPSILON_SVR">EPSILON_SVR</option>
142 <option value="C_SVC">C_SVC</option>
143 </param>
144 <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) "/>
145 <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p) "/>
146 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
147 <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
148 <option value="LINEAR">LINEAR</option>
149 <option value="RBF">RBF</option>
150 <option value="POLY">POLY</option>
151 <option value="OLIGO">OLIGO</option>
152 </param>
153 <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) "/>
154 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
155 <param name="param_max_std" type="float" min="0.0" optional="True" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help="(-max_std) "/>
156 <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) "/>
157 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
158 <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help="(-total_gradient_time) "/>
159 <param name="param_first_dim_rt" type="boolean" truevalue="-first_dim_rt" falsevalue="" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt) "/>
160 <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 &lt;br&gt;with the step size to get the new value" help="(-additive_cv) "/>
161 <param name="param_cv_skip_cv" type="boolean" truevalue="-cv:skip_cv" falsevalue="" checked="false" optional="True" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help="(-skip_cv) "/>
162 <param name="param_cv_number_of_runs" type="integer" min="1" optional="True" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help="(-number_of_runs) "/>
163 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
164 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
165 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
166 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
167 <param name="param_cv_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start) "/>
168 <param name="param_cv_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size) "/>
169 <param name="param_cv_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop) "/>
170 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
171 <param name="param_cv_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size) "/>
172 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
173 <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
174 <param name="param_cv_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size) "/>
175 <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop) "/>
176 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
177 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
178 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
179 <expand macro="advanced_options">
180 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
181 </expand>
182 </inputs>
183 <outputs>
184 <data name="param_out" format="txt"/>
185 </outputs>
186 <help>**What it does**
187
188 Trains a model for the retention time prediction of peptides from a training set.
189
190
191 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
192 <expand macro="references"/>
193 </tool>