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comparison RTModel.xml @ 0:8480765683cf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:32:28 -0500
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children b68f859bd5f3
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-1:000000000000 0:8480765683cf
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <tool id="RTModel" name="RTModel" version="2.1.0">
5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
6 <macros>
7 <token name="@EXECUTABLE@">RTModel</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RTModel
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_in_positive:
19 -in_positive $param_in_positive
20 #end if
21 #if $param_in_negative:
22 -in_negative $param_in_negative
23 #end if
24 #if $param_out:
25 -out $param_out
26 #end if
27 #if $param_svm_type:
28 -svm_type $param_svm_type
29 #end if
30 #if $param_nu:
31 -nu $param_nu
32 #end if
33 #if $param_p:
34 -p $param_p
35 #end if
36 #if $param_c:
37 -c $param_c
38 #end if
39 #if $param_kernel_type:
40 -kernel_type $param_kernel_type
41 #end if
42 #if $param_degree:
43 -degree $param_degree
44 #end if
45 #if $param_border_length:
46 -border_length $param_border_length
47 #end if
48 #if $param_max_std:
49 -max_std $param_max_std
50 #end if
51 #if $param_k_mer_length:
52 -k_mer_length $param_k_mer_length
53 #end if
54 #if $param_sigma:
55 -sigma $param_sigma
56 #end if
57 #if $param_total_gradient_time:
58 -total_gradient_time $param_total_gradient_time
59 #end if
60 #if $param_first_dim_rt:
61 -first_dim_rt
62 #end if
63 #if $param_additive_cv:
64 -additive_cv
65 #end if
66 #if $param_cv_skip_cv:
67 -cv:skip_cv
68 #end if
69 #if $param_cv_number_of_runs:
70 -cv:number_of_runs $param_cv_number_of_runs
71 #end if
72 #if $param_cv_number_of_partitions:
73 -cv:number_of_partitions $param_cv_number_of_partitions
74 #end if
75 #if $param_cv_degree_start:
76 -cv:degree_start $param_cv_degree_start
77 #end if
78 #if $param_cv_degree_step_size:
79 -cv:degree_step_size $param_cv_degree_step_size
80 #end if
81 #if $param_cv_degree_stop:
82 -cv:degree_stop $param_cv_degree_stop
83 #end if
84 #if $param_cv_p_start:
85 -cv:p_start $param_cv_p_start
86 #end if
87 #if $param_cv_p_step_size:
88 -cv:p_step_size $param_cv_p_step_size
89 #end if
90 #if $param_cv_p_stop:
91 -cv:p_stop $param_cv_p_stop
92 #end if
93 #if $param_cv_c_start:
94 -cv:c_start $param_cv_c_start
95 #end if
96 #if $param_cv_c_step_size:
97 -cv:c_step_size $param_cv_c_step_size
98 #end if
99 #if $param_cv_c_stop:
100 -cv:c_stop $param_cv_c_stop
101 #end if
102 #if $param_cv_nu_start:
103 -cv:nu_start $param_cv_nu_start
104 #end if
105 #if $param_cv_nu_step_size:
106 -cv:nu_step_size $param_cv_nu_step_size
107 #end if
108 #if $param_cv_nu_stop:
109 -cv:nu_stop $param_cv_nu_stop
110 #end if
111 #if $param_cv_sigma_start:
112 -cv:sigma_start $param_cv_sigma_start
113 #end if
114 #if $param_cv_sigma_step_size:
115 -cv:sigma_step_size $param_cv_sigma_step_size
116 #end if
117 #if $param_cv_sigma_stop:
118 -cv:sigma_stop $param_cv_sigma_stop
119 #end if
120 #if $adv_opts.adv_opts_selector=='advanced':
121 #if $adv_opts.param_force:
122 -force
123 #end if
124 #end if
125 </command>
126 <inputs>
127 <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;"/>
128 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/>
129 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/>
130 <param name="param_svm_type" display="radio" type="select" optional="False" 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) ">
131 <option value="NU_SVR" selected="true">NU_SVR</option>
132 <option value="NU_SVC">NU_SVC</option>
133 <option value="EPSILON_SVR">EPSILON_SVR</option>
134 <option value="C_SVC">C_SVC</option>
135 </param>
136 <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) "/>
137 <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p) "/>
138 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
139 <param name="param_kernel_type" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
140 <option value="LINEAR">LINEAR</option>
141 <option value="RBF">RBF</option>
142 <option value="POLY">POLY</option>
143 <option value="OLIGO" selected="true">OLIGO</option>
144 </param>
145 <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) "/>
146 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
147 <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) "/>
148 <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) "/>
149 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
150 <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) "/>
151 <param name="param_first_dim_rt" display="radio" 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) "/>
152 <param name="param_additive_cv" display="radio" 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) "/>
153 <param name="param_cv_skip_cv" display="radio" 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) "/>
154 <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) "/>
155 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
156 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
157 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
158 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
159 <param name="param_cv_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start) "/>
160 <param name="param_cv_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size) "/>
161 <param name="param_cv_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop) "/>
162 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
163 <param name="param_cv_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size) "/>
164 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
165 <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) "/>
166 <param name="param_cv_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size) "/>
167 <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) "/>
168 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
169 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
170 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
171 <expand macro="advanced_options">
172 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
173 </expand>
174 </inputs>
175 <outputs>
176 <data name="param_out" format="txt"/>
177 </outputs>
178 <help>Trains a model for the retention time prediction of peptides from a training set.
179
180
181 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
182 </tool>