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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
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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="RTModel" name="RTModel" 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 retention time prediction of peptides from a training set.</description> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <macros> 4 <tool id="RTModel" name="RTModel" version="2.0.0">
5 <token name="@EXECUTABLE@">RTModel</token> 5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">RTModel</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>RTModel 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>RTModel
11 14
12 -in ${param_in} 15 #if $param_in:
13 -in_positive ${param_in_positive} 16 -in $param_in
14 -in_negative ${param_in_negative} 17 #end if
15 -out ${param_out} 18 #if $param_in_positive:
16 -svm_type ${param_svm_type} 19 -in_positive $param_in_positive
17 -nu ${param_nu} 20 #end if
18 -p ${param_p} 21 #if $param_in_negative:
19 -c ${param_c} 22 -in_negative $param_in_negative
20 -kernel_type ${param_kernel_type} 23 #end if
21 -degree ${param_degree} 24 #if $param_out:
22 -border_length ${param_border_length} 25 -out $param_out
23 -max_std ${param_max_std} 26 #end if
24 -k_mer_length ${param_k_mer_length} 27 #if $param_svm_type:
25 -sigma ${param_sigma} 28 -svm_type
26 -total_gradient_time ${param_total_gradient_time} 29 #if &quot; &quot; in str($param_svm_type):
27 ${param_first_dim_rt} 30 &quot;$param_svm_type&quot;
28 ${param_additive_cv} 31 #else
29 -threads \${GALAXY_SLOTS:-24} 32 $param_svm_type
30 ${param_skip_cv} 33 #end if
31 -cv:number_of_runs ${param_number_of_runs} 34 #end if
32 -cv:number_of_partitions ${param_number_of_partitions} 35 #if $param_nu:
33 -cv:degree_start ${param_degree_start} 36 -nu $param_nu
34 -cv:degree_step_size ${param_degree_step_size} 37 #end if
35 -cv:degree_stop ${param_degree_stop} 38 #if $param_p:
36 -cv:p_start ${param_p_start} 39 -p $param_p
37 -cv:p_step_size ${param_p_step_size} 40 #end if
38 -cv:p_stop ${param_p_stop} 41 #if $param_c:
39 -cv:c_start ${param_c_start} 42 -c $param_c
40 -cv:c_step_size ${param_c_step_size} 43 #end if
41 -cv:c_stop ${param_c_stop} 44 #if $param_kernel_type:
42 -cv:nu_start ${param_nu_start} 45 -kernel_type
43 -cv:nu_step_size ${param_nu_step_size} 46 #if &quot; &quot; in str($param_kernel_type):
44 -cv:nu_stop ${param_nu_stop} 47 &quot;$param_kernel_type&quot;
45 -cv:sigma_start ${param_sigma_start} 48 #else
46 -cv:sigma_step_size ${param_sigma_step_size} 49 $param_kernel_type
47 -cv:sigma_stop ${param_sigma_stop} 50 #end if
51 #end if
52 #if $param_degree:
53 -degree $param_degree
54 #end if
55 #if $param_border_length:
56 -border_length $param_border_length
57 #end if
58 #if $param_max_std:
59 -max_std $param_max_std
60 #end if
61 #if $param_k_mer_length:
62 -k_mer_length $param_k_mer_length
63 #end if
64 #if $param_sigma:
65 -sigma $param_sigma
66 #end if
67 #if $param_total_gradient_time:
68 -total_gradient_time $param_total_gradient_time
69 #end if
70 #if $param_first_dim_rt:
71 -first_dim_rt
72 #end if
73 #if $param_additive_cv:
74 -additive_cv
75 #end if
76 -threads \${GALAXY_SLOTS:-24}
77 #if $param_cv_skip_cv:
78 -cv:skip_cv
79 #end if
80 #if $param_cv_number_of_runs:
81 -cv:number_of_runs $param_cv_number_of_runs
82 #end if
83 #if $param_cv_number_of_partitions:
84 -cv:number_of_partitions $param_cv_number_of_partitions
85 #end if
86 #if $param_cv_degree_start:
87 -cv:degree_start $param_cv_degree_start
88 #end if
89 #if $param_cv_degree_step_size:
90 -cv:degree_step_size $param_cv_degree_step_size
91 #end if
92 #if $param_cv_degree_stop:
93 -cv:degree_stop $param_cv_degree_stop
94 #end if
95 #if $param_cv_p_start:
96 -cv:p_start $param_cv_p_start
97 #end if
98 #if $param_cv_p_step_size:
99 -cv:p_step_size $param_cv_p_step_size
100 #end if
101 #if $param_cv_p_stop:
102 -cv:p_stop $param_cv_p_stop
103 #end if
104 #if $param_cv_c_start:
105 -cv:c_start $param_cv_c_start
106 #end if
107 #if $param_cv_c_step_size:
108 -cv:c_step_size $param_cv_c_step_size
109 #end if
110 #if $param_cv_c_stop:
111 -cv:c_stop $param_cv_c_stop
112 #end if
113 #if $param_cv_nu_start:
114 -cv:nu_start $param_cv_nu_start
115 #end if
116 #if $param_cv_nu_step_size:
117 -cv:nu_step_size $param_cv_nu_step_size
118 #end if
119 #if $param_cv_nu_stop:
120 -cv:nu_stop $param_cv_nu_stop
121 #end if
122 #if $param_cv_sigma_start:
123 -cv:sigma_start $param_cv_sigma_start
124 #end if
125 #if $param_cv_sigma_step_size:
126 -cv:sigma_step_size $param_cv_sigma_step_size
127 #end if
128 #if $param_cv_sigma_stop:
129 -cv:sigma_stop $param_cv_sigma_stop
130 #end if
131 #if $adv_opts.adv_opts_selector=='advanced':
132 #if $adv_opts.param_force:
133 -force
134 #end if
135 #end if
48 </command> 136 </command>
49 <inputs> 137 <inputs>
50 <param name="param_in" type="data" format="idXML,txt" optional="True" label="This is the name of the input file (RT prediction). 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.#br#" help="(-in)"/> 138 <param format="xml,txt" 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;" label="This is the name of the input file (RT prediction)" name="param_in" optional="True" type="data"/>
51 <param name="param_in_positive" type="data" format="idXML" optional="True" label="input file with positive examples (peptide separation prediction)#br#" help="(-in_positive)"/> 139 <param format="xml" help="(-in_positive) " label="input file with positive examples (peptide separation prediction)" name="param_in_positive" optional="True" type="data"/>
52 <param name="param_in_negative" type="data" format="idXML" optional="True" label="input file with negative examples (peptide separation prediction)#br#" help="(-in_negative)"/> 140 <param format="xml" help="(-in_negative) " label="input file with negative examples (peptide separation prediction)" name="param_in_negative" optional="True" type="data"/>
53 <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#br#to C_SVC for separation prediction)#br#" help="(-svm_type)"> 141 <param help="(-svm_type) " 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)" name="param_svm_type" optional="True" type="select" value="NU_SVR">
54 <option value="NU_SVR">NU_SVR</option> 142 <option value="NU_SVR">NU_SVR</option>
55 <option value="NU_SVC">NU_SVC</option> 143 <option value="NU_SVC">NU_SVC</option>
56 <option value="EPSILON_SVR">EPSILON_SVR</option> 144 <option value="EPSILON_SVR">EPSILON_SVR</option>
57 <option value="C_SVC">C_SVC</option> 145 <option value="C_SVC">C_SVC</option>
58 </param> 146 </param>
59 <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)"/> 147 <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"/>
60 <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p)"/> 148 <param help="(-p) " label="the epsilon parameter of the svm (for epsilon-SVR)" name="param_p" type="float" value="0.1"/>
61 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c)"/> 149 <param help="(-c) " label="the penalty parameter of the svm" name="param_c" type="float" value="1.0"/>
62 <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type)"> 150 <param help="(-kernel_type) " label="the kernel type of the svm" name="param_kernel_type" optional="True" type="select" value="OLIGO">
63 <option value="LINEAR">LINEAR</option> 151 <option value="LINEAR">LINEAR</option>
64 <option value="RBF">RBF</option> 152 <option value="RBF">RBF</option>
65 <option value="POLY">POLY</option> 153 <option value="POLY">POLY</option>
66 <option value="OLIGO">OLIGO</option> 154 <option value="OLIGO">OLIGO</option>
67 </param> 155 </param>
68 <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)#br#" help="(-degree)"/> 156 <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"/>
69 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length)"/> 157 <param help="(-border_length) " label="length of the POBK" min="1" name="param_border_length" optional="True" type="integer" value="22"/>
70 <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)"/> 158 <param help="(-max_std) " label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" min="0.0" name="param_max_std" optional="True" type="float" value="10.0"/>
71 <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)"/> 159 <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"/>
72 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma)"/> 160 <param help="(-sigma) " label="sigma of the POBK" name="param_sigma" type="float" value="5.0"/>
73 <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)"/> 161 <param help="(-total_gradient_time) " label="the time (in seconds) of the gradient (only for RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
74 <param name="param_first_dim_rt" type="boolean" truevalue="-first_dim_rt true" falsevalue="-first_dim_rt false" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt)"/> 162 <param checked="false" falsevalue="" help="(-first_dim_rt) " label="if set the model will be built for first_dim_rt" name="param_first_dim_rt" optional="True" truevalue="-first_dim_rt" type="boolean"/>
75 <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#br#with the step size to get the new value" help="(-additive_cv)"/> 163 <param checked="false" falsevalue="" help="(-additive_cv) " 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" name="param_additive_cv" optional="True" truevalue="-additive_cv" type="boolean"/>
76 <param name="param_skip_cv" type="boolean" truevalue="-cv:skip_cv true" falsevalue="-cv:skip_cv false" 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)"/> 164 <param checked="false" falsevalue="" help="(-skip_cv) " label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" name="param_cv_skip_cv" optional="True" truevalue="-cv:skip_cv" type="boolean"/>
77 <param name="param_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)"/> 165 <param help="(-number_of_runs) " label="number of runs for the CV (each run creates a new random partition of the data)" min="1" name="param_cv_number_of_runs" optional="True" type="integer" value="1"/>
78 <param name="param_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions)"/> 166 <param help="(-number_of_partitions) " label="number of CV partitions" min="2" name="param_cv_number_of_partitions" optional="True" type="integer" value="10"/>
79 <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/> 167 <param help="(-degree_start) " label="starting point of degree" min="1" name="param_cv_degree_start" optional="True" type="integer" value="1"/>
80 <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/> 168 <param help="(-degree_step_size) " label="step size point of degree" name="param_cv_degree_step_size" type="integer" value="2"/>
81 <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/> 169 <param help="(-degree_stop) " label="stopping point of degree" name="param_cv_degree_stop" type="integer" value="4"/>
82 <param name="param_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start)"/> 170 <param help="(-p_start) " label="starting point of p" name="param_cv_p_start" type="float" value="1.0"/>
83 <param name="param_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size)"/> 171 <param help="(-p_step_size) " label="step size point of p" name="param_cv_p_step_size" type="float" value="10.0"/>
84 <param name="param_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop)"/> 172 <param help="(-p_stop) " label="stopping point of p" name="param_cv_p_stop" type="float" value="1000.0"/>
85 <param name="param_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start)"/> 173 <param help="(-c_start) " label="starting point of c" name="param_cv_c_start" type="float" value="1.0"/>
86 <param name="param_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size)"/> 174 <param help="(-c_step_size) " label="step size of c" name="param_cv_c_step_size" type="float" value="10.0"/>
87 <param name="param_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop)"/> 175 <param help="(-c_stop) " label="stopping point of c" name="param_cv_c_stop" type="float" value="1000.0"/>
88 <param name="param_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start)"/> 176 <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="0.3"/>
89 <param name="param_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size)"/> 177 <param help="(-nu_step_size) " label="step size of nu" name="param_cv_nu_step_size" type="float" value="1.2"/>
90 <param name="param_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop)"/> 178 <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="0.7"/>
91 <param name="param_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start)"/> 179 <param help="(-sigma_start) " label="starting point of sigma" name="param_cv_sigma_start" type="float" value="1.0"/>
92 <param name="param_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size)"/> 180 <param help="(-sigma_step_size) " label="step size of sigma" name="param_cv_sigma_step_size" type="float" value="1.3"/>
93 <param name="param_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop)"/> 181 <param help="(-sigma_stop) " label="stopping point of sigma" name="param_cv_sigma_stop" type="float" value="15.0"/>
94 </inputs> 182 <expand macro="advanced_options">
95 <outputs> 183 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
96 <data name="param_out" label="output file: the model in libsvm format" format="txt"/> 184 </expand>
97 </outputs> 185 </inputs>
98 <help>**What it does** 186 <outputs>
99 187 <data format="txt" name="param_out"/>
100 Trains a model for the retention time prediction of peptides from a training set. 188 </outputs>
189 <help>Trains a model for the retention time prediction of peptides from a training set.
101 190
102 191
103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html 192 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
104 193 </tool>
105 @REFERENCES@
106 </help>
107 </tool>