Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer

annotate SvmTheoreticalSpectrumGeneratorTrainer.xml @ 5:6d9c00e778ff 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 13:04:23 -0500
parents be688ba2bc09
children e98ae1229a67
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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: [Utilities]-->
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4 <tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="2.3.0">
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5 <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</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>SvmTheoreticalSpectrumGeneratorTrainer
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14
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15 #if $param_in_spectra:
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16 -in_spectra $param_in_spectra
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17 #end if
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18 #if $param_in_identifications:
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19 -in_identifications $param_in_identifications
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20 #end if
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21 #if $param_model_output_file:
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22 -model_output_file $param_model_output_file
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23 #end if
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24 #if $param_precursor_charge:
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25 -precursor_charge $param_precursor_charge
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26 #end if
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27 #if $param_write_training_files:
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28 -write_training_files
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29 #end if
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30 #if $param_algorithm_number_intensity_levels:
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31 -algorithm:number_intensity_levels $param_algorithm_number_intensity_levels
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32 #end if
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33 #if $param_algorithm_number_regions:
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34 -algorithm:number_regions $param_algorithm_number_regions
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35 #end if
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36 #if $param_algorithm_parent_tolerance:
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37 -algorithm:parent_tolerance $param_algorithm_parent_tolerance
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38 #end if
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39 #if $param_algorithm_peak_tolerance:
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40 -algorithm:peak_tolerance $param_algorithm_peak_tolerance
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41 #end if
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42 #if $param_algorithm_add_b_ions:
1
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43 -algorithm:add_b_ions
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44 #if " " in str($param_algorithm_add_b_ions):
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45 "$param_algorithm_add_b_ions"
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46 #else
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47 $param_algorithm_add_b_ions
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48 #end if
0
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49 #end if
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50 #if $param_algorithm_add_y_ions:
1
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51 -algorithm:add_y_ions
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52 #if " " in str($param_algorithm_add_y_ions):
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53 "$param_algorithm_add_y_ions"
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54 #else
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55 $param_algorithm_add_y_ions
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56 #end if
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57 #end if
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58 #if $param_algorithm_add_a_ions:
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59 -algorithm:add_a_ions
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60 #end if
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61 #if $param_algorithm_add_c_ions:
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62 -algorithm:add_c_ions
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63 #end if
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64 #if $param_algorithm_add_x_ions:
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65 -algorithm:add_x_ions
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66 #end if
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67 #if $param_algorithm_add_z_ions:
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68 -algorithm:add_z_ions
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69 #end if
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70 #if $param_algorithm_add_losses:
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71 -algorithm:add_losses
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72 #end if
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73 #if $param_algorithm_add_b2_ions:
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74 -algorithm:add_b2_ions
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75 #end if
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76 #if $param_algorithm_add_y2_ions:
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77 -algorithm:add_y2_ions
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78 #end if
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79 #if $param_algorithm_svm_svc_type:
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80 -algorithm:svm:svc_type $param_algorithm_svm_svc_type
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81 #end if
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82 #if $param_algorithm_svm_svr_type:
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83 -algorithm:svm:svr_type $param_algorithm_svm_svr_type
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84 #end if
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85 #if $param_algorithm_svm_scaling:
1
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86 -algorithm:svm:scaling
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87 #if " " in str($param_algorithm_svm_scaling):
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88 "$param_algorithm_svm_scaling"
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89 #else
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90 $param_algorithm_svm_scaling
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91 #end if
0
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92 #end if
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93 #if $param_algorithm_svm_scaling_lower:
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94 -algorithm:svm:scaling_lower $param_algorithm_svm_scaling_lower
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95 #end if
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96 #if $param_algorithm_svm_scaling_upper:
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97 -algorithm:svm:scaling_upper $param_algorithm_svm_scaling_upper
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98 #end if
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99 #if $param_algorithm_svm_n_fold:
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100 -algorithm:svm:n_fold $param_algorithm_svm_n_fold
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101 #end if
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102 #if $param_algorithm_svm_grid:
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103 -algorithm:svm:grid
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104 #end if
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105 #if $param_algorithm_svm_additive_cv:
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106 -algorithm:svm:additive_cv
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107 #end if
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108 #if $param_algorithm_svm_svc_kernel_type:
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109 -algorithm:svm:svc:kernel_type $param_algorithm_svm_svc_kernel_type
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110 #end if
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111 #if $param_algorithm_svm_svc_degree:
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112 -algorithm:svm:svc:degree $param_algorithm_svm_svc_degree
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113 #end if
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114 #if $param_algorithm_svm_svc_gamma:
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115 -algorithm:svm:svc:gamma $param_algorithm_svm_svc_gamma
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116 #end if
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117 #if $param_algorithm_svm_svc_C:
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118 -algorithm:svm:svc:C $param_algorithm_svm_svc_C
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119 #end if
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120 #if $param_algorithm_svm_svc_nu:
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121 -algorithm:svm:svc:nu $param_algorithm_svm_svc_nu
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122 #end if
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123 #if $param_algorithm_svm_svc_balancing:
1
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124 -algorithm:svm:svc:balancing
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125 #if " " in str($param_algorithm_svm_svc_balancing):
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126 "$param_algorithm_svm_svc_balancing"
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127 #else
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128 $param_algorithm_svm_svc_balancing
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129 #end if
0
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130 #end if
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131 #if $param_algorithm_svm_svc_degree_start:
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132 -algorithm:svm:svc:degree_start $param_algorithm_svm_svc_degree_start
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133 #end if
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134 #if $param_algorithm_svm_svc_degree_step_size:
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135 -algorithm:svm:svc:degree_step_size $param_algorithm_svm_svc_degree_step_size
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136 #end if
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137 #if $param_algorithm_svm_svc_degree_stop:
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138 -algorithm:svm:svc:degree_stop $param_algorithm_svm_svc_degree_stop
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139 #end if
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140 #if $param_algorithm_svm_svc_gamma_start:
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141 -algorithm:svm:svc:gamma_start $param_algorithm_svm_svc_gamma_start
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142 #end if
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143 #if $param_algorithm_svm_svc_gamma_step_size:
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144 -algorithm:svm:svc:gamma_step_size $param_algorithm_svm_svc_gamma_step_size
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145 #end if
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146 #if $param_algorithm_svm_svc_gamma_stop:
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147 -algorithm:svm:svc:gamma_stop $param_algorithm_svm_svc_gamma_stop
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148 #end if
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149 #if $param_algorithm_svm_svc_c_start:
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150 -algorithm:svm:svc:c_start $param_algorithm_svm_svc_c_start
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151 #end if
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152 #if $param_algorithm_svm_svc_c_step_size:
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153 -algorithm:svm:svc:c_step_size $param_algorithm_svm_svc_c_step_size
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154 #end if
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155 #if $param_algorithm_svm_svc_c_stop:
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156 -algorithm:svm:svc:c_stop $param_algorithm_svm_svc_c_stop
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157 #end if
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158 #if $param_algorithm_svm_svc_nu_start:
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159 -algorithm:svm:svc:nu_start $param_algorithm_svm_svc_nu_start
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160 #end if
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161 #if $param_algorithm_svm_svc_nu_step_size:
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162 -algorithm:svm:svc:nu_step_size $param_algorithm_svm_svc_nu_step_size
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163 #end if
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164 #if $param_algorithm_svm_svc_nu_stop:
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165 -algorithm:svm:svc:nu_stop $param_algorithm_svm_svc_nu_stop
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166 #end if
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167 #if $param_algorithm_svm_svr_kernel_type:
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168 -algorithm:svm:svr:kernel_type $param_algorithm_svm_svr_kernel_type
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169 #end if
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170 #if $param_algorithm_svm_svr_degree:
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171 -algorithm:svm:svr:degree $param_algorithm_svm_svr_degree
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172 #end if
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173 #if $param_algorithm_svm_svr_gamma:
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174 -algorithm:svm:svr:gamma $param_algorithm_svm_svr_gamma
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175 #end if
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176 #if $param_algorithm_svm_svr_C:
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177 -algorithm:svm:svr:C $param_algorithm_svm_svr_C
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178 #end if
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179 #if $param_algorithm_svm_svr_p:
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180 -algorithm:svm:svr:p $param_algorithm_svm_svr_p
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181 #end if
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182 #if $param_algorithm_svm_svr_nu:
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183 -algorithm:svm:svr:nu $param_algorithm_svm_svr_nu
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184 #end if
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185 #if $param_algorithm_svm_svr_degree_start:
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186 -algorithm:svm:svr:degree_start $param_algorithm_svm_svr_degree_start
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187 #end if
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188 #if $param_algorithm_svm_svr_degree_step_size:
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189 -algorithm:svm:svr:degree_step_size $param_algorithm_svm_svr_degree_step_size
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190 #end if
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191 #if $param_algorithm_svm_svr_degree_stop:
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192 -algorithm:svm:svr:degree_stop $param_algorithm_svm_svr_degree_stop
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193 #end if
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194 #if $param_algorithm_svm_svr_gamma_start:
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195 -algorithm:svm:svr:gamma_start $param_algorithm_svm_svr_gamma_start
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196 #end if
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197 #if $param_algorithm_svm_svr_gamma_step_size:
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198 -algorithm:svm:svr:gamma_step_size $param_algorithm_svm_svr_gamma_step_size
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199 #end if
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200 #if $param_algorithm_svm_svr_gamma_stop:
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201 -algorithm:svm:svr:gamma_stop $param_algorithm_svm_svr_gamma_stop
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202 #end if
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203 #if $param_algorithm_svm_svr_p_start:
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204 -algorithm:svm:svr:p_start $param_algorithm_svm_svr_p_start
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205 #end if
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206 #if $param_algorithm_svm_svr_p_step_size:
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207 -algorithm:svm:svr:p_step_size $param_algorithm_svm_svr_p_step_size
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208 #end if
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209 #if $param_algorithm_svm_svr_p_stop:
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210 -algorithm:svm:svr:p_stop $param_algorithm_svm_svr_p_stop
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211 #end if
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212 #if $param_algorithm_svm_svr_c_start:
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213 -algorithm:svm:svr:c_start $param_algorithm_svm_svr_c_start
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214 #end if
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215 #if $param_algorithm_svm_svr_c_step_size:
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216 -algorithm:svm:svr:c_step_size $param_algorithm_svm_svr_c_step_size
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217 #end if
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218 #if $param_algorithm_svm_svr_c_stop:
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219 -algorithm:svm:svr:c_stop $param_algorithm_svm_svr_c_stop
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220 #end if
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221 #if $param_algorithm_svm_svr_nu_start:
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222 -algorithm:svm:svr:nu_start $param_algorithm_svm_svr_nu_start
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223 #end if
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224 #if $param_algorithm_svm_svr_nu_step_size:
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225 -algorithm:svm:svr:nu_step_size $param_algorithm_svm_svr_nu_step_size
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226 #end if
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227 #if $param_algorithm_svm_svr_nu_stop:
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228 -algorithm:svm:svr:nu_stop $param_algorithm_svm_svr_nu_stop
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229 #end if
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230 #if $adv_opts.adv_opts_selector=='advanced':
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231 #if $adv_opts.param_force:
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232 -force
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233 #end if
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234 #end if
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235 </command>
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236 <inputs>
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237 <param name="param_in_spectra" type="data" format="mzml" optional="False" label="Input Training Spectra in mzML" help="(-in_spectra) "/>
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238 <param name="param_in_identifications" type="data" format="idxml" optional="False" label="Input file with corresponding sequences in idXML" help="(-in_identifications) "/>
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239 <param name="param_precursor_charge" type="integer" min="1" max="3" optional="True" value="2" label="Precursor charge state used for model training" help="(-precursor_charge) "/>
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240 <param name="param_write_training_files" display="radio" type="boolean" truevalue="-write_training_files" falsevalue="" checked="false" optional="True" label="No models are trained but input training files for libSVM command line tools are produced" help="(-write_training_files) "/>
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241 <param name="param_algorithm_number_intensity_levels" type="integer" value="7" label="The number of intensity bins (for secondary type models)" help="(-number_intensity_levels) "/>
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242 <param name="param_algorithm_number_regions" type="integer" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help="(-number_regions) "/>
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243 <param name="param_algorithm_parent_tolerance" type="float" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help="(-parent_tolerance) "/>
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244 <param name="param_algorithm_peak_tolerance" type="float" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help="(-peak_tolerance) "/>
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245 <param name="param_algorithm_add_b_ions" display="radio" type="select" optional="False" value="true" label="Train simulator for b-ions" help="(-add_b_ions) ">
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246 <option value="true" selected="true">true</option>
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247 <option value="false">false</option>
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248 </param>
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249 <param name="param_algorithm_add_y_ions" display="radio" type="select" optional="False" value="true" label="Train simulator for y-ions" help="(-add_y_ions) ">
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250 <option value="true" selected="true">true</option>
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251 <option value="false">false</option>
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252 </param>
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253 <param name="param_algorithm_add_a_ions" display="radio" type="boolean" truevalue="-algorithm:add_a_ions" falsevalue="" checked="false" optional="True" label="Train simulator for a-ions" help="(-add_a_ions) "/>
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254 <param name="param_algorithm_add_c_ions" display="radio" type="boolean" truevalue="-algorithm:add_c_ions" falsevalue="" checked="false" optional="True" label="Train simulator for c-ions" help="(-add_c_ions) "/>
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255 <param name="param_algorithm_add_x_ions" display="radio" type="boolean" truevalue="-algorithm:add_x_ions" falsevalue="" checked="false" optional="True" label="Train simulator for x-ions" help="(-add_x_ions) "/>
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256 <param name="param_algorithm_add_z_ions" display="radio" type="boolean" truevalue="-algorithm:add_z_ions" falsevalue="" checked="false" optional="True" label="Train simulator for z-ions" help="(-add_z_ions) "/>
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257 <param name="param_algorithm_add_losses" display="radio" type="boolean" truevalue="-algorithm:add_losses" falsevalue="" checked="false" optional="True" label="Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions" help="(-add_losses) "/>
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258 <param name="param_algorithm_add_b2_ions" display="radio" type="boolean" truevalue="-algorithm:add_b2_ions" falsevalue="" checked="false" optional="True" label="Train simulator for doubly charged b-ions" help="(-add_b2_ions) "/>
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259 <param name="param_algorithm_add_y2_ions" display="radio" type="boolean" truevalue="-algorithm:add_y2_ions" falsevalue="" checked="false" optional="True" label="Train simulator for double charged y-ions" help="(-add_y2_ions) "/>
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260 <param name="param_algorithm_svm_svc_type" type="integer" min="0" max="1" optional="True" value="0" label="Type of the SVC: 0=C_SVC 1=NU_SVC" help="(-svc_type) "/>
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261 <param name="param_algorithm_svm_svr_type" type="integer" min="0" max="1" optional="True" value="1" label="Type of the SVR: 0=EPSILON_SVR 1=NU_SVR" help="(-svr_type) "/>
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262 <param name="param_algorithm_svm_scaling" display="radio" type="select" optional="False" value="true" label="Apply scaling of feature values" help="(-scaling) ">
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263 <option value="true" selected="true">true</option>
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264 <option value="false">false</option>
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265 </param>
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266 <param name="param_algorithm_svm_scaling_lower" type="float" value="0.0" label="Lower bound for scaling" help="(-scaling_lower) "/>
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267 <param name="param_algorithm_svm_scaling_upper" type="float" value="1.0" label="Upper bound for scaling" help="(-scaling_upper) "/>
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268 <param name="param_algorithm_svm_n_fold" type="integer" min="1" optional="True" value="5" label="n_fold cross validation is performed" help="(-n_fold) "/>
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269 <param name="param_algorithm_svm_grid" display="radio" type="boolean" truevalue="-algorithm:svm:grid" falsevalue="" checked="false" optional="True" label="Perform grid search" help="(-grid) "/>
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270 <param name="param_algorithm_svm_additive_cv" display="radio" type="boolean" truevalue="-algorithm:svm:additive_cv" falsevalue="" checked="false" optional="True" label="Additive step size (if false multiplicative)" help="(-additive_cv) "/>
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271 <param name="param_algorithm_svm_svc_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type) "/>
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272 <param name="param_algorithm_svm_svc_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree) "/>
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273 <param name="param_algorithm_svm_svc_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma) "/>
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274 <param name="param_algorithm_svm_svc_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C) "/>
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275 <param name="param_algorithm_svm_svc_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu) "/>
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276 <param name="param_algorithm_svm_svc_balancing" display="radio" type="select" optional="False" value="true" label="Use class balanced SVC training" help="(-balancing) ">
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277 <option value="true" selected="true">true</option>
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278 <option value="false">false</option>
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279 </param>
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280 <param name="param_algorithm_svm_svc_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
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281 <param name="param_algorithm_svm_svc_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
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282 <param name="param_algorithm_svm_svc_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
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283 <param name="param_algorithm_svm_svc_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start) "/>
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284 <param name="param_algorithm_svm_svc_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size) "/>
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285 <param name="param_algorithm_svm_svc_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop) "/>
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286 <param name="param_algorithm_svm_svc_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start) "/>
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287 <param name="param_algorithm_svm_svc_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size) "/>
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288 <param name="param_algorithm_svm_svc_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop) "/>
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289 <param name="param_algorithm_svm_svc_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
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290 <param name="param_algorithm_svm_svc_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size) "/>
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291 <param name="param_algorithm_svm_svc_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop) "/>
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292 <param name="param_algorithm_svm_svr_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type) "/>
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293 <param name="param_algorithm_svm_svr_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree) "/>
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294 <param name="param_algorithm_svm_svr_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma) "/>
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295 <param name="param_algorithm_svm_svr_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C) "/>
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296 <param name="param_algorithm_svm_svr_p" type="float" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help="(-p) "/>
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297 <param name="param_algorithm_svm_svr_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu) "/>
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298 <param name="param_algorithm_svm_svr_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/>
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299 <param name="param_algorithm_svm_svr_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
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300 <param name="param_algorithm_svm_svr_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
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301 <param name="param_algorithm_svm_svr_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start) "/>
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302 <param name="param_algorithm_svm_svr_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size) "/>
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303 <param name="param_algorithm_svm_svr_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop) "/>
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304 <param name="param_algorithm_svm_svr_p_start" type="float" value="1e-05" label="starting point of p" help="(-p_start) "/>
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305 <param name="param_algorithm_svm_svr_p_step_size" type="integer" value="100" label="step size point of p" help="(-p_step_size) "/>
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306 <param name="param_algorithm_svm_svr_p_stop" type="float" value="0.1" label="stopping point of p" help="(-p_stop) "/>
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307 <param name="param_algorithm_svm_svr_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start) "/>
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308 <param name="param_algorithm_svm_svr_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size) "/>
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309 <param name="param_algorithm_svm_svr_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop) "/>
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310 <param name="param_algorithm_svm_svr_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
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311 <param name="param_algorithm_svm_svr_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size) "/>
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312 <param name="param_algorithm_svm_svr_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop) "/>
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313 <expand macro="advanced_options">
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314 <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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315 </expand>
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316 </inputs>
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317 <outputs>
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318 <data name="param_model_output_file" format="data"/>
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319 </outputs>
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320 <help>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
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321
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322
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323 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html</help>
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324 </tool>