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comparison PTModel.xml @ 0:2b34b435c177 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 12:34:29 -0500
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-1:000000000000 0:2b34b435c177
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="PTModel" name="PTModel" version="2.1.0">
5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
6 <macros>
7 <token name="@EXECUTABLE@">PTModel</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PTModel
14
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_c:
25 -c $param_c
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_kernel_type:
34 -kernel_type $param_kernel_type
35 #end if
36 #if $param_degree:
37 -degree $param_degree
38 #end if
39 #if $param_border_length:
40 -border_length $param_border_length
41 #end if
42 #if $param_k_mer_length:
43 -k_mer_length $param_k_mer_length
44 #end if
45 #if $param_sigma:
46 -sigma $param_sigma
47 #end if
48 #if $param_max_positive_count:
49 -max_positive_count $param_max_positive_count
50 #end if
51 #if $param_max_negative_count:
52 -max_negative_count $param_max_negative_count
53 #end if
54 #if $param_redundant:
55 -redundant
56 #end if
57 #if $param_additive_cv:
58 -additive_cv
59 #end if
60 #if $param_cv_skip_cv:
61 -cv:skip_cv
62 #end if
63 #if $param_cv_number_of_runs:
64 -cv:number_of_runs $param_cv_number_of_runs
65 #end if
66 #if $param_cv_number_of_partitions:
67 -cv:number_of_partitions $param_cv_number_of_partitions
68 #end if
69 #if $param_cv_degree_start:
70 -cv:degree_start $param_cv_degree_start
71 #end if
72 #if $param_cv_degree_step_size:
73 -cv:degree_step_size $param_cv_degree_step_size
74 #end if
75 #if $param_cv_degree_stop:
76 -cv:degree_stop $param_cv_degree_stop
77 #end if
78 #if $param_cv_c_start:
79 -cv:c_start $param_cv_c_start
80 #end if
81 #if $param_cv_c_step_size:
82 -cv:c_step_size $param_cv_c_step_size
83 #end if
84 #if $param_cv_c_stop:
85 -cv:c_stop $param_cv_c_stop
86 #end if
87 #if $param_cv_nu_start:
88 -cv:nu_start $param_cv_nu_start
89 #end if
90 #if $param_cv_nu_step_size:
91 -cv:nu_step_size $param_cv_nu_step_size
92 #end if
93 #if $param_cv_nu_stop:
94 -cv:nu_stop $param_cv_nu_stop
95 #end if
96 #if $param_cv_sigma_start:
97 -cv:sigma_start $param_cv_sigma_start
98 #end if
99 #if $param_cv_sigma_step_size:
100 -cv:sigma_step_size $param_cv_sigma_step_size
101 #end if
102 #if $param_cv_sigma_stop:
103 -cv:sigma_stop $param_cv_sigma_stop
104 #end if
105 #if $adv_opts.adv_opts_selector=='advanced':
106 #if $adv_opts.param_force:
107 -force
108 #end if
109 #end if
110 </command>
111 <inputs>
112 <param name="param_in_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/>
113 <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/>
114 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
115 <param name="param_svm_type" display="radio" type="select" optional="False" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) ">
116 <option value="NU_SVC">NU_SVC</option>
117 <option value="C_SVC" selected="true">C_SVC</option>
118 </param>
119 <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) "/>
120 <param name="param_kernel_type" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
121 <option value="LINEAR">LINEAR</option>
122 <option value="RBF">RBF</option>
123 <option value="POLY">POLY</option>
124 <option value="OLIGO" selected="true">OLIGO</option>
125 </param>
126 <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) "/>
127 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
128 <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) "/>
129 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
130 <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) "/>
131 <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) "/>
132 <param name="param_redundant" display="radio" 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) "/>
133 <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 with the step size to get the new value" help="(-additive_cv) "/>
134 <param name="param_cv_skip_cv" display="radio" 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) "/>
135 <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) "/>
136 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
137 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
138 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
139 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
140 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
141 <param name="param_cv_c_step_size" type="float" value="100.0" label="step size of c" help="(-c_step_size) "/>
142 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
143 <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) "/>
144 <param name="param_cv_nu_step_size" type="float" value="1.3" label="step size of nu" help="(-nu_step_size) "/>
145 <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) "/>
146 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
147 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
148 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
149 <expand macro="advanced_options">
150 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
151 </expand>
152 </inputs>
153 <outputs>
154 <data name="param_out" format="txt"/>
155 </outputs>
156 <help>Trains a model for the prediction of proteotypic peptides from a training set.
157
158
159 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help>
160 </tool>