Mercurial > repos > galaxyp > openms_ptmodel

annotate PTModel.xml @ 5:a174f62788b7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:14:53 -0500
parents 30ccca244091
children 88bd406e3b22
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2b34b435c177 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Peptide property prediction]-->
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4 <tool id="PTModel" name="PTModel" version="2.3.0">
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5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PTModel</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>PTModel
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14
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15 #if $param_in_positive:
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16 -in_positive $param_in_positive
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17 #end if
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18 #if $param_in_negative:
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19 -in_negative $param_in_negative
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_c:
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25 -c $param_c
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26 #end if
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27 #if $param_svm_type:
1
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28 -svm_type
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29 #if " " in str($param_svm_type):
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30 "$param_svm_type"
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31 #else
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32 $param_svm_type
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33 #end if
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34 #end if
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35 #if $param_nu:
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36 -nu $param_nu
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37 #end if
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38 #if $param_kernel_type:
1
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39 -kernel_type
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40 #if " " in str($param_kernel_type):
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41 "$param_kernel_type"
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42 #else
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43 $param_kernel_type
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44 #end if
0
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45 #end if
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46 #if $param_degree:
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47 -degree $param_degree
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48 #end if
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49 #if $param_border_length:
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50 -border_length $param_border_length
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51 #end if
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52 #if $param_k_mer_length:
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53 -k_mer_length $param_k_mer_length
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54 #end if
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55 #if $param_sigma:
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56 -sigma $param_sigma
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57 #end if
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58 #if $param_max_positive_count:
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59 -max_positive_count $param_max_positive_count
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60 #end if
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61 #if $param_max_negative_count:
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62 -max_negative_count $param_max_negative_count
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63 #end if
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64 #if $param_redundant:
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65 -redundant
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66 #end if
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67 #if $param_additive_cv:
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68 -additive_cv
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69 #end if
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70 #if $param_cv_skip_cv:
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71 -cv:skip_cv
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72 #end if
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73 #if $param_cv_number_of_runs:
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74 -cv:number_of_runs $param_cv_number_of_runs
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75 #end if
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76 #if $param_cv_number_of_partitions:
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77 -cv:number_of_partitions $param_cv_number_of_partitions
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78 #end if
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79 #if $param_cv_degree_start:
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80 -cv:degree_start $param_cv_degree_start
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81 #end if
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82 #if $param_cv_degree_step_size:
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83 -cv:degree_step_size $param_cv_degree_step_size
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84 #end if
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85 #if $param_cv_degree_stop:
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86 -cv:degree_stop $param_cv_degree_stop
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87 #end if
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88 #if $param_cv_c_start:
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89 -cv:c_start $param_cv_c_start
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90 #end if
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91 #if $param_cv_c_step_size:
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92 -cv:c_step_size $param_cv_c_step_size
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93 #end if
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94 #if $param_cv_c_stop:
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95 -cv:c_stop $param_cv_c_stop
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96 #end if
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97 #if $param_cv_nu_start:
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98 -cv:nu_start $param_cv_nu_start
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99 #end if
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100 #if $param_cv_nu_step_size:
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101 -cv:nu_step_size $param_cv_nu_step_size
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102 #end if
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103 #if $param_cv_nu_stop:
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104 -cv:nu_stop $param_cv_nu_stop
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105 #end if
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106 #if $param_cv_sigma_start:
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107 -cv:sigma_start $param_cv_sigma_start
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108 #end if
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109 #if $param_cv_sigma_step_size:
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110 -cv:sigma_step_size $param_cv_sigma_step_size
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111 #end if
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112 #if $param_cv_sigma_stop:
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113 -cv:sigma_stop $param_cv_sigma_stop
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114 #end if
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115 #if $adv_opts.adv_opts_selector=='advanced':
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116 #if $adv_opts.param_force:
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117 -force
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118 #end if
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119 #end if
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120 </command>
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121 <inputs>
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122 <param name="param_in_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/>
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123 <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/>
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124 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
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125 <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) ">
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126 <option value="NU_SVC">NU_SVC</option>
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127 <option value="C_SVC" selected="true">C_SVC</option>
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128 </param>
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129 <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) "/>
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130 <param name="param_kernel_type" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) ">
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131 <option value="LINEAR">LINEAR</option>
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132 <option value="RBF">RBF</option>
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133 <option value="POLY">POLY</option>
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134 <option value="OLIGO" selected="true">OLIGO</option>
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135 </param>
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136 <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) "/>
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137 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/>
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138 <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) "/>
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139 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
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140 <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) "/>
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141 <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) "/>
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142 <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) "/>
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143 <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) "/>
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144 <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) "/>
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145 <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) "/>
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146 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/>
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147 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
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148 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
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149 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
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150 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
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151 <param name="param_cv_c_step_size" type="float" value="100.0" label="step size of c" help="(-c_step_size) "/>
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152 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
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153 <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) "/>
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154 <param name="param_cv_nu_step_size" type="float" value="1.3" label="step size of nu" help="(-nu_step_size) "/>
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155 <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) "/>
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156 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
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157 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
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158 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
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159 <expand macro="advanced_options">
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160 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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161 </expand>
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162 </inputs>
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163 <outputs>
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164 <data name="param_out" format="txt"/>
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165 </outputs>
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166 <help>Trains a model for the prediction of proteotypic peptides from a training set.
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169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help>
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170 </tool>