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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="PTModel" name="PTModel" version="1.12.0"> 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 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <macros> 4 <tool id="PTModel" name="PTModel" version="2.0.0">
5 <token name="@EXECUTABLE@">PTModel</token> 5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">PTModel</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>PTModel 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>PTModel
11 14
12 -in_positive ${param_in_positive} 15 #if $param_in_positive:
13 -in_negative ${param_in_negative} 16 -in_positive $param_in_positive
14 -out ${param_out} 17 #end if
15 -c ${param_c} 18 #if $param_in_negative:
16 -svm_type ${param_svm_type} 19 -in_negative $param_in_negative
17 -nu ${param_nu} 20 #end if
18 -kernel_type ${param_kernel_type} 21 #if $param_out:
19 -degree ${param_degree} 22 -out $param_out
20 -border_length ${param_border_length} 23 #end if
21 -k_mer_length ${param_k_mer_length} 24 #if $param_c:
22 -sigma ${param_sigma} 25 -c $param_c
23 -max_positive_count ${param_max_positive_count} 26 #end if
24 -max_negative_count ${param_max_negative_count} 27 #if $param_svm_type:
25 ${param_redundant} 28 -svm_type
26 ${param_additive_cv} 29 #if &quot; &quot; in str($param_svm_type):
27 -threads \${GALAXY_SLOTS:-24} 30 &quot;$param_svm_type&quot;
28 ${param_skip_cv} 31 #else
29 -cv:number_of_runs ${param_number_of_runs} 32 $param_svm_type
30 -cv:number_of_partitions ${param_number_of_partitions} 33 #end if
31 -cv:degree_start ${param_degree_start} 34 #end if
32 -cv:degree_step_size ${param_degree_step_size} 35 #if $param_nu:
33 -cv:degree_stop ${param_degree_stop} 36 -nu $param_nu
34 -cv:c_start ${param_c_start} 37 #end if
35 -cv:c_step_size ${param_c_step_size} 38 #if $param_kernel_type:
36 -cv:c_stop ${param_c_stop} 39 -kernel_type
37 -cv:nu_start ${param_nu_start} 40 #if &quot; &quot; in str($param_kernel_type):
38 -cv:nu_step_size ${param_nu_step_size} 41 &quot;$param_kernel_type&quot;
39 -cv:nu_stop ${param_nu_stop} 42 #else
40 -cv:sigma_start ${param_sigma_start} 43 $param_kernel_type
41 -cv:sigma_step_size ${param_sigma_step_size} 44 #end if
42 -cv:sigma_stop ${param_sigma_stop} 45 #end if
46 #if $param_degree:
47 -degree $param_degree
48 #end if
49 #if $param_border_length:
50 -border_length $param_border_length
51 #end if
52 #if $param_k_mer_length:
53 -k_mer_length $param_k_mer_length
54 #end if
55 #if $param_sigma:
56 -sigma $param_sigma
57 #end if
58 #if $param_max_positive_count:
59 -max_positive_count $param_max_positive_count
60 #end if
61 #if $param_max_negative_count:
62 -max_negative_count $param_max_negative_count
63 #end if
64 #if $param_redundant:
65 -redundant
66 #end if
67 #if $param_additive_cv:
68 -additive_cv
69 #end if
70 -threads \${GALAXY_SLOTS:-24}
71 #if $param_cv_skip_cv:
72 -cv:skip_cv
73 #end if
74 #if $param_cv_number_of_runs:
75 -cv:number_of_runs $param_cv_number_of_runs
76 #end if
77 #if $param_cv_number_of_partitions:
78 -cv:number_of_partitions $param_cv_number_of_partitions
79 #end if
80 #if $param_cv_degree_start:
81 -cv:degree_start $param_cv_degree_start
82 #end if
83 #if $param_cv_degree_step_size:
84 -cv:degree_step_size $param_cv_degree_step_size
85 #end if
86 #if $param_cv_degree_stop:
87 -cv:degree_stop $param_cv_degree_stop
88 #end if
89 #if $param_cv_c_start:
90 -cv:c_start $param_cv_c_start
91 #end if
92 #if $param_cv_c_step_size:
93 -cv:c_step_size $param_cv_c_step_size
94 #end if
95 #if $param_cv_c_stop:
96 -cv:c_stop $param_cv_c_stop
97 #end if
98 #if $param_cv_nu_start:
99 -cv:nu_start $param_cv_nu_start
100 #end if
101 #if $param_cv_nu_step_size:
102 -cv:nu_step_size $param_cv_nu_step_size
103 #end if
104 #if $param_cv_nu_stop:
105 -cv:nu_stop $param_cv_nu_stop
106 #end if
107 #if $param_cv_sigma_start:
108 -cv:sigma_start $param_cv_sigma_start
109 #end if
110 #if $param_cv_sigma_step_size:
111 -cv:sigma_step_size $param_cv_sigma_step_size
112 #end if
113 #if $param_cv_sigma_stop:
114 -cv:sigma_stop $param_cv_sigma_stop
115 #end if
116 #if $adv_opts.adv_opts_selector=='advanced':
117 #if $adv_opts.param_force:
118 -force
119 #end if
120 #end if
43 </command> 121 </command>
44 <inputs> 122 <inputs>
45 <param name="param_in_positive" type="data" format="idXML" optional="False" label="input file with positive examples" help="(-in_positive)"/> 123 <param format="xml" help="(-in_positive) " label="input file with positive examples" name="param_in_positive" optional="False" type="data"/>
46 <param name="param_in_negative" type="data" format="idXML" optional="False" label="input file with negative examples" help="(-in_negative)"/> 124 <param format="xml" help="(-in_negative) " label="input file with negative examples" name="param_in_negative" optional="False" type="data"/>
47 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c)"/> 125 <param help="(-c) " label="the penalty parameter of the svm" name="param_c" type="float" value="1.0"/>
48 <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)"> 126 <param help="(-svm_type) " label="the type of the svm (NU_SVC or C_SVC)" name="param_svm_type" optional="True" type="select" value="C_SVC">
49 <option value="NU_SVC">NU_SVC</option> 127 <option value="NU_SVC">NU_SVC</option>
50 <option value="C_SVC">C_SVC</option> 128 <option value="C_SVC">C_SVC</option>
51 </param> 129 </param>
52 <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)"/> 130 <param help="(-nu) " label="the nu parameter [0..1] of the svm (for nu-SVR)" max="1.0" min="0.0" name="param_nu" optional="True" type="float" value="0.5"/>
53 <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type)"> 131 <param help="(-kernel_type) " label="the kernel type of the svm" name="param_kernel_type" optional="True" type="select" value="OLIGO">
54 <option value="LINEAR">LINEAR</option> 132 <option value="LINEAR">LINEAR</option>
55 <option value="RBF">RBF</option> 133 <option value="RBF">RBF</option>
56 <option value="POLY">POLY</option> 134 <option value="POLY">POLY</option>
57 <option value="OLIGO">OLIGO</option> 135 <option value="OLIGO">OLIGO</option>
58 </param> 136 </param>
59 <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)"/> 137 <param help="(-degree) " label="the degree parameter of the kernel function of the svm (POLY kernel)" min="1" name="param_degree" optional="True" type="integer" value="1"/>
60 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length)"/> 138 <param help="(-border_length) " label="length of the POBK" min="1" name="param_border_length" optional="True" type="integer" value="22"/>
61 <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)"/> 139 <param help="(-k_mer_length) " label="k_mer length of the POBK" min="1" name="param_k_mer_length" optional="True" type="integer" value="1"/>
62 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma)"/> 140 <param help="(-sigma) " label="sigma of the POBK" name="param_sigma" type="float" value="5.0"/>
63 <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)"/> 141 <param help="(-max_positive_count) " label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" min="1" name="param_max_positive_count" optional="True" type="integer" value="1000"/>
64 <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)"/> 142 <param help="(-max_negative_count) " label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" min="1" name="param_max_negative_count" optional="True" type="integer" value="1000"/>
65 <param name="param_redundant" type="boolean" truevalue="-redundant true" falsevalue="-redundant false" 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)"/> 143 <param checked="false" falsevalue="" help="(-redundant) " 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" name="param_redundant" optional="True" truevalue="-redundant" type="boolean"/>
66 <param name="param_additive_cv" type="boolean" truevalue="-additive_cv true" falsevalue="-additive_cv false" 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)"/> 144 <param checked="false" falsevalue="" help="(-additive_cv) " label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value" name="param_additive_cv" optional="True" truevalue="-additive_cv" type="boolean"/>
67 <param name="param_skip_cv" type="boolean" truevalue="-cv:skip_cv true" falsevalue="-cv:skip_cv false" 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)"/> 145 <param checked="false" falsevalue="" help="(-skip_cv) " label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" name="param_cv_skip_cv" optional="True" truevalue="-cv:skip_cv" type="boolean"/>
68 <param name="param_number_of_runs" type="integer" min="1" optional="True" value="10" label="number of runs for the CV" help="(-number_of_runs)"/> 146 <param help="(-number_of_runs) " label="number of runs for the CV" min="1" name="param_cv_number_of_runs" optional="True" type="integer" value="10"/>
69 <param name="param_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions)"/> 147 <param help="(-number_of_partitions) " label="number of CV partitions" min="2" name="param_cv_number_of_partitions" optional="True" type="integer" value="10"/>
70 <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/> 148 <param help="(-degree_start) " label="starting point of degree" min="1" name="param_cv_degree_start" optional="True" type="integer" value="1"/>
71 <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/> 149 <param help="(-degree_step_size) " label="step size point of degree" name="param_cv_degree_step_size" type="integer" value="2"/>
72 <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/> 150 <param help="(-degree_stop) " label="stopping point of degree" name="param_cv_degree_stop" type="integer" value="4"/>
73 <param name="param_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start)"/> 151 <param help="(-c_start) " label="starting point of c" name="param_cv_c_start" type="float" value="1.0"/>
74 <param name="param_c_step_size" type="float" value="100.0" label="step size of c" help="(-c_step_size)"/> 152 <param help="(-c_step_size) " label="step size of c" name="param_cv_c_step_size" type="float" value="100.0"/>
75 <param name="param_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop)"/> 153 <param help="(-c_stop) " label="stopping point of c" name="param_cv_c_stop" type="float" value="1000.0"/>
76 <param name="param_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="starting point of nu" help="(-nu_start)"/> 154 <param help="(-nu_start) " label="starting point of nu" max="1.0" min="0.0" name="param_cv_nu_start" optional="True" type="float" value="0.1"/>
77 <param name="param_nu_step_size" type="float" value="1.3" label="step size of nu" help="(-nu_step_size)"/> 155 <param help="(-nu_step_size) " label="step size of nu" name="param_cv_nu_step_size" type="float" value="1.3"/>
78 <param name="param_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.9" label="stopping point of nu" help="(-nu_stop)"/> 156 <param help="(-nu_stop) " label="stopping point of nu" max="1.0" min="0.0" name="param_cv_nu_stop" optional="True" type="float" value="0.9"/>
79 <param name="param_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start)"/> 157 <param help="(-sigma_start) " label="starting point of sigma" name="param_cv_sigma_start" type="float" value="1.0"/>
80 <param name="param_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size)"/> 158 <param help="(-sigma_step_size) " label="step size of sigma" name="param_cv_sigma_step_size" type="float" value="1.3"/>
81 <param name="param_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop)"/> 159 <param help="(-sigma_stop) " label="stopping point of sigma" name="param_cv_sigma_stop" type="float" value="15.0"/>
82 </inputs> 160 <expand macro="advanced_options">
83 <outputs> 161 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
84 <data name="param_out" label="output file: the model in libsvm format" format="txt"/> 162 </expand>
85 </outputs> 163 </inputs>
86 <help>**What it does** 164 <outputs>
87 165 <data format="txt" name="param_out"/>
88 Trains a model for the prediction of proteotypic peptides from a training set. 166 </outputs>
167 <help>Trains a model for the prediction of proteotypic peptides from a training set.
89 168
90 169
91 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html 170 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help>
92 171 </tool>
93 @REFERENCES@
94 </help>
95 </tool>