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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="1.12.0">
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3 <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>SvmTheoreticalSpectrumGeneratorTrainer
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11
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12 -in_spectra ${param_in_spectra}
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13 -in_identifications ${param_in_identifications}
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14 -model_output_file ${param_model_output_file}
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15 -precursor_charge ${param_precursor_charge}
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16 ${param_write_training_files}
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17 -threads \${GALAXY_SLOTS:-24}
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18 -algorithm:number_intensity_levels ${param_number_intensity_levels}
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19 -algorithm:number_regions ${param_number_regions}
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20 -algorithm:parent_tolerance ${param_parent_tolerance}
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21 -algorithm:peak_tolerance ${param_peak_tolerance}
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22 ${param_add_b_ions}
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23 ${param_add_y_ions}
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24 ${param_add_a_ions}
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25 ${param_add_c_ions}
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26 ${param_add_x_ions}
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27 ${param_add_z_ions}
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28 ${param_add_losses}
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29 ${param_add_b2_ions}
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30 ${param_add_y2_ions}
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31 -algorithm:svm:svc_type ${param_svc_type}
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32 -algorithm:svm:svr_type ${param_svr_type}
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33 ${param_scaling}
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34 -algorithm:svm:scaling_lower ${param_scaling_lower}
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35 -algorithm:svm:scaling_upper ${param_scaling_upper}
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36 -algorithm:svm:n_fold ${param_n_fold}
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37 ${param_grid}
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38 ${param_additive_cv}
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39 -algorithm:svm:svc:kernel_type ${param_kernel_type}
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40 -algorithm:svm:svc:degree ${param_degree}
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41 -algorithm:svm:svc:gamma ${param_gamma}
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42 -algorithm:svm:svc:C ${param_C}
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43 -algorithm:svm:svc:nu ${param_nu}
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44 ${param_balancing}
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45 -algorithm:svm:svc:degree_start ${param_degree_start}
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46 -algorithm:svm:svc:degree_step_size ${param_degree_step_size}
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47 -algorithm:svm:svc:degree_stop ${param_degree_stop}
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48 -algorithm:svm:svc:gamma_start ${param_gamma_start}
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49 -algorithm:svm:svc:gamma_step_size ${param_gamma_step_size}
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50 -algorithm:svm:svc:gamma_stop ${param_gamma_stop}
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51 -algorithm:svm:svc:c_start ${param_c_start}
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52 -algorithm:svm:svc:c_step_size ${param_c_step_size}
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53 -algorithm:svm:svc:c_stop ${param_c_stop}
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54 -algorithm:svm:svc:nu_start ${param_nu_start}
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55 -algorithm:svm:svc:nu_step_size ${param_nu_step_size}
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56 -algorithm:svm:svc:nu_stop ${param_nu_stop}
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57 -algorithm:svm:svr:kernel_type ${param_kernel_type}
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58 -algorithm:svm:svr:degree ${param_degree}
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59 -algorithm:svm:svr:gamma ${param_gamma}
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60 -algorithm:svm:svr:C ${param_C}
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61 -algorithm:svm:svr:p ${param_p}
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62 -algorithm:svm:svr:nu ${param_nu}
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63 -algorithm:svm:svr:degree_start ${param_degree_start}
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64 -algorithm:svm:svr:degree_step_size ${param_degree_step_size}
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65 -algorithm:svm:svr:degree_stop ${param_degree_stop}
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66 -algorithm:svm:svr:gamma_start ${param_gamma_start}
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67 -algorithm:svm:svr:gamma_step_size ${param_gamma_step_size}
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68 -algorithm:svm:svr:gamma_stop ${param_gamma_stop}
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69 -algorithm:svm:svr:p_start ${param_p_start}
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70 -algorithm:svm:svr:p_step_size ${param_p_step_size}
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71 -algorithm:svm:svr:p_stop ${param_p_stop}
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72 -algorithm:svm:svr:c_start ${param_c_start}
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73 -algorithm:svm:svr:c_step_size ${param_c_step_size}
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74 -algorithm:svm:svr:c_stop ${param_c_stop}
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75 -algorithm:svm:svr:nu_start ${param_nu_start}
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76 -algorithm:svm:svr:nu_step_size ${param_nu_step_size}
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77 -algorithm:svm:svr:nu_stop ${param_nu_stop}
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78 </command>
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79 <inputs>
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80 <param name="param_in_spectra" type="data" format="mzML" optional="False" label="Input Training Spectra in mzML" help="(-in_spectra)"/>
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81 <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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82 <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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83 <param name="param_write_training_files" type="boolean" truevalue="-write_training_files true" falsevalue="-write_training_files false" 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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84 <param name="param_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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85 <param name="param_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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86 <param name="param_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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87 <param name="param_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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88 <param name="param_add_b_ions" type="boolean" truevalue="-algorithm:add_b_ions true" falsevalue="-algorithm:add_b_ions false" checked="true" optional="True" label="Train simulator for b-ions" help="(-add_b_ions)"/>
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89 <param name="param_add_y_ions" type="boolean" truevalue="-algorithm:add_y_ions true" falsevalue="-algorithm:add_y_ions false" checked="true" optional="True" label="Train simulator for y-ions" help="(-add_y_ions)"/>
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90 <param name="param_add_a_ions" type="boolean" truevalue="-algorithm:add_a_ions true" falsevalue="-algorithm:add_a_ions false" checked="false" optional="True" label="Train simulator for a-ions" help="(-add_a_ions)"/>
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91 <param name="param_add_c_ions" type="boolean" truevalue="-algorithm:add_c_ions true" falsevalue="-algorithm:add_c_ions false" checked="false" optional="True" label="Train simulator for c-ions" help="(-add_c_ions)"/>
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92 <param name="param_add_x_ions" type="boolean" truevalue="-algorithm:add_x_ions true" falsevalue="-algorithm:add_x_ions false" checked="false" optional="True" label="Train simulator for x-ions" help="(-add_x_ions)"/>
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93 <param name="param_add_z_ions" type="boolean" truevalue="-algorithm:add_z_ions true" falsevalue="-algorithm:add_z_ions false" checked="false" optional="True" label="Train simulator for z-ions" help="(-add_z_ions)"/>
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94 <param name="param_add_losses" type="boolean" truevalue="-algorithm:add_losses true" falsevalue="-algorithm:add_losses false" 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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95 <param name="param_add_b2_ions" type="boolean" truevalue="-algorithm:add_b2_ions true" falsevalue="-algorithm:add_b2_ions false" checked="false" optional="True" label="Train simulator for doubly charged b-ions" help="(-add_b2_ions)"/>
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96 <param name="param_add_y2_ions" type="boolean" truevalue="-algorithm:add_y2_ions true" falsevalue="-algorithm:add_y2_ions false" checked="false" optional="True" label="Train simulator for double charged y-ions" help="(-add_y2_ions)"/>
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97 <param name="param_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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98 <param name="param_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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99 <param name="param_scaling" type="boolean" truevalue="-algorithm:svm:scaling true" falsevalue="-algorithm:svm:scaling false" checked="true" optional="True" label="Apply scaling of feature values" help="(-scaling)"/>
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100 <param name="param_scaling_lower" type="float" value="0.0" label="Lower bound for scaling" help="(-scaling_lower)"/>
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101 <param name="param_scaling_upper" type="float" value="1.0" label="Upper bound for scaling" help="(-scaling_upper)"/>
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102 <param name="param_n_fold" type="integer" min="1" optional="True" value="5" label="n_fold cross validation is performed" help="(-n_fold)"/>
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103 <param name="param_grid" type="boolean" truevalue="-algorithm:svm:grid true" falsevalue="-algorithm:svm:grid false" checked="false" optional="True" label="Perform grid search" help="(-grid)"/>
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104 <param name="param_additive_cv" type="boolean" truevalue="-algorithm:svm:additive_cv true" falsevalue="-algorithm:svm:additive_cv false" checked="false" optional="True" label="Additive step size (if false multiplicative)" help="(-additive_cv)"/>
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105 <param name="param_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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106 <param name="param_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree)"/>
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107 <param name="param_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma)"/>
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108 <param name="param_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C)"/>
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109 <param name="param_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu)"/>
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110 <param name="param_balancing" type="boolean" truevalue="-algorithm:svm:svc:balancing true" falsevalue="-algorithm:svm:svc:balancing false" checked="true" optional="True" label="Use class balanced SVC training" help="(-balancing)"/>
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111 <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/>
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112 <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
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113 <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
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114 <param name="param_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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115 <param name="param_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size)"/>
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116 <param name="param_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop)"/>
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117 <param name="param_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start)"/>
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118 <param name="param_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size)"/>
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119 <param name="param_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop)"/>
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120 <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)"/>
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121 <param name="param_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size)"/>
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122 <param name="param_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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123 <param name="param_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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124 <param name="param_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree)"/>
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125 <param name="param_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma)"/>
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126 <param name="param_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C)"/>
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127 <param name="param_p" type="float" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help="(-p)"/>
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128 <param name="param_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu)"/>
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129 <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/>
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130 <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
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131 <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
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132 <param name="param_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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133 <param name="param_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size)"/>
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134 <param name="param_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop)"/>
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135 <param name="param_p_start" type="float" value="1e-05" label="starting point of p" help="(-p_start)"/>
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136 <param name="param_p_step_size" type="integer" value="100" label="step size point of p" help="(-p_step_size)"/>
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137 <param name="param_p_stop" type="float" value="0.1" label="stopping point of p" help="(-p_stop)"/>
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138 <param name="param_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start)"/>
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139 <param name="param_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size)"/>
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140 <param name="param_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop)"/>
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141 <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)"/>
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142 <param name="param_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size)"/>
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143 <param name="param_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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144 </inputs>
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145 <outputs>
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146 <data name="param_model_output_file" label="Name for output files. For each ion_type one file <filename>_residue_loss_charge.svm and one <filename>.info which has to be passed to the SvmTheoretical SpectrumGenerator" format="data"/>
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147 </outputs>
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148 <help>**What it does**
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149
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150 Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
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151
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152
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153 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html
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154
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155 @REFERENCES@
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156 </help>
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157 </tool>
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