Mercurial > repos > galaxyp > openms_rtmodel

annotate RTModel.xml @ 2:5412fdc499b6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:23:06 -0400
parents b68f859bd5f3
children c3da4387e137
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8480765683cf 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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Peptide property prediction]-->
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4 <tool id="RTModel" name="RTModel" version="2.2.0">
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5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RTModel</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>RTModel
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_in_positive:
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19 -in_positive $param_in_positive
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20 #end if
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21 #if $param_in_negative:
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22 -in_negative $param_in_negative
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23 #end if
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24 #if $param_out:
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25 -out $param_out
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26 #end if
1
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27 #if $param_out_oligo_params:
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28 -out_oligo_params $param_out_oligo_params
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29 #end if
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30 #if $param_out_oligo_trainset:
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31 -out_oligo_trainset $param_out_oligo_trainset
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32 #end if
0
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33 #if $param_svm_type:
1
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34 -svm_type
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35 #if " " in str($param_svm_type):
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36 "$param_svm_type"
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37 #else
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38 $param_svm_type
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39 #end if
0
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40 #end if
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41 #if $param_nu:
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42 -nu $param_nu
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43 #end if
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44 #if $param_p:
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45 -p $param_p
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46 #end if
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47 #if $param_c:
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48 -c $param_c
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49 #end if
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50 #if $param_kernel_type:
1
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51 -kernel_type
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52 #if " " in str($param_kernel_type):
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53 "$param_kernel_type"
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54 #else
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55 $param_kernel_type
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56 #end if
0
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57 #end if
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58 #if $param_degree:
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59 -degree $param_degree
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60 #end if
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61 #if $param_border_length:
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62 -border_length $param_border_length
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63 #end if
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64 #if $param_max_std:
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65 -max_std $param_max_std
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66 #end if
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67 #if $param_k_mer_length:
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68 -k_mer_length $param_k_mer_length
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69 #end if
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70 #if $param_sigma:
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71 -sigma $param_sigma
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72 #end if
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73 #if $param_total_gradient_time:
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74 -total_gradient_time $param_total_gradient_time
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75 #end if
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76 #if $param_first_dim_rt:
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77 -first_dim_rt
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78 #end if
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79 #if $param_additive_cv:
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80 -additive_cv
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81 #end if
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82 #if $param_cv_skip_cv:
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83 -cv:skip_cv
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84 #end if
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85 #if $param_cv_number_of_runs:
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86 -cv:number_of_runs $param_cv_number_of_runs
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87 #end if
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88 #if $param_cv_number_of_partitions:
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89 -cv:number_of_partitions $param_cv_number_of_partitions
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90 #end if
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91 #if $param_cv_degree_start:
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92 -cv:degree_start $param_cv_degree_start
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93 #end if
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94 #if $param_cv_degree_step_size:
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95 -cv:degree_step_size $param_cv_degree_step_size
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96 #end if
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97 #if $param_cv_degree_stop:
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98 -cv:degree_stop $param_cv_degree_stop
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99 #end if
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100 #if $param_cv_p_start:
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101 -cv:p_start $param_cv_p_start
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102 #end if
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103 #if $param_cv_p_step_size:
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104 -cv:p_step_size $param_cv_p_step_size
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105 #end if
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106 #if $param_cv_p_stop:
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107 -cv:p_stop $param_cv_p_stop
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108 #end if
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109 #if $param_cv_c_start:
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110 -cv:c_start $param_cv_c_start
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111 #end if
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112 #if $param_cv_c_step_size:
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113 -cv:c_step_size $param_cv_c_step_size
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114 #end if
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115 #if $param_cv_c_stop:
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116 -cv:c_stop $param_cv_c_stop
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117 #end if
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118 #if $param_cv_nu_start:
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119 -cv:nu_start $param_cv_nu_start
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120 #end if
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121 #if $param_cv_nu_step_size:
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122 -cv:nu_step_size $param_cv_nu_step_size
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123 #end if
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124 #if $param_cv_nu_stop:
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125 -cv:nu_stop $param_cv_nu_stop
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126 #end if
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127 #if $param_cv_sigma_start:
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128 -cv:sigma_start $param_cv_sigma_start
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129 #end if
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130 #if $param_cv_sigma_step_size:
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131 -cv:sigma_step_size $param_cv_sigma_step_size
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132 #end if
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133 #if $param_cv_sigma_stop:
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134 -cv:sigma_stop $param_cv_sigma_stop
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135 #end if
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136 #if $adv_opts.adv_opts_selector=='advanced':
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137 #if $adv_opts.param_force:
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138 -force
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139 #end if
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140 #end if
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141 </command>
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142 <inputs>
1
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143 <param name="param_in" type="data" format="idxml,txt" optional="True" label="This is the name of the input file (RT prediction)" 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;"/>
0
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144 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/>
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145 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/>
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146 <param name="param_svm_type" display="radio" type="select" optional="False" value="NU_SVR" 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)" help="(-svm_type) ">
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147 <option value="NU_SVR" selected="true">NU_SVR</option>
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148 <option value="NU_SVC">NU_SVC</option>
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149 <option value="EPSILON_SVR">EPSILON_SVR</option>
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150 <option value="C_SVC">C_SVC</option>
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151 </param>
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152 <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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153 <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p) "/>
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154 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
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155 <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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156 <option value="LINEAR">LINEAR</option>
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157 <option value="RBF">RBF</option>
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158 <option value="POLY">POLY</option>
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159 <option value="OLIGO" selected="true">OLIGO</option>
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160 </param>
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161 <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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162 <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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163 <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) "/>
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164 <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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165 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/>
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166 <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) "/>
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167 <param name="param_first_dim_rt" display="radio" type="boolean" truevalue="-first_dim_rt" falsevalue="" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt) "/>
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168 <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 &lt;br&gt;with the step size to get the new value" help="(-additive_cv) "/>
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169 <param name="param_cv_skip_cv" display="radio" type="boolean" truevalue="-cv:skip_cv" falsevalue="" 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) "/>
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170 <param name="param_cv_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) "/>
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171 <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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172 <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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173 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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174 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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175 <param name="param_cv_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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176 <param name="param_cv_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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177 <param name="param_cv_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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178 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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179 <param name="param_cv_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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180 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/>
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181 <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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182 <param name="param_cv_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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183 <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop) "/>
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184 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/>
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185 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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186 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/>
8480765683cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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187 <expand macro="advanced_options">
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188 <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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189 </expand>
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190 </inputs>
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191 <outputs>
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192 <data name="param_out" format="txt"/>
1
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193 <data name="param_out_oligo_params" format="paramXML"/>
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194 <data name="param_out_oligo_trainset" format="txt"/>
0
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195 </outputs>
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196 <help>Trains a model for the retention time prediction of peptides from a training set.
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197
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198
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199 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
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200 </tool>