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annotate RTModel.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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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="2.0.0">
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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
0
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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
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27 #if $param_svm_type:
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28 -svm_type
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29 #if &quot; &quot; in str($param_svm_type):
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30 &quot;$param_svm_type&quot;
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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_p:
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39 -p $param_p
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40 #end if
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41 #if $param_c:
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42 -c $param_c
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43 #end if
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44 #if $param_kernel_type:
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45 -kernel_type
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46 #if &quot; &quot; in str($param_kernel_type):
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47 &quot;$param_kernel_type&quot;
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48 #else
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49 $param_kernel_type
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50 #end if
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51 #end if
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52 #if $param_degree:
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53 -degree $param_degree
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54 #end if
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55 #if $param_border_length:
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56 -border_length $param_border_length
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57 #end if
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58 #if $param_max_std:
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59 -max_std $param_max_std
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60 #end if
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61 #if $param_k_mer_length:
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62 -k_mer_length $param_k_mer_length
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63 #end if
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64 #if $param_sigma:
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65 -sigma $param_sigma
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66 #end if
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67 #if $param_total_gradient_time:
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68 -total_gradient_time $param_total_gradient_time
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69 #end if
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70 #if $param_first_dim_rt:
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71 -first_dim_rt
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72 #end if
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73 #if $param_additive_cv:
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74 -additive_cv
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75 #end if
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76 -threads \${GALAXY_SLOTS:-24}
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77 #if $param_cv_skip_cv:
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78 -cv:skip_cv
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79 #end if
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80 #if $param_cv_number_of_runs:
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81 -cv:number_of_runs $param_cv_number_of_runs
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82 #end if
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83 #if $param_cv_number_of_partitions:
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84 -cv:number_of_partitions $param_cv_number_of_partitions
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85 #end if
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86 #if $param_cv_degree_start:
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87 -cv:degree_start $param_cv_degree_start
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88 #end if
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89 #if $param_cv_degree_step_size:
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90 -cv:degree_step_size $param_cv_degree_step_size
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91 #end if
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92 #if $param_cv_degree_stop:
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93 -cv:degree_stop $param_cv_degree_stop
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94 #end if
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95 #if $param_cv_p_start:
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96 -cv:p_start $param_cv_p_start
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97 #end if
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98 #if $param_cv_p_step_size:
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99 -cv:p_step_size $param_cv_p_step_size
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100 #end if
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101 #if $param_cv_p_stop:
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102 -cv:p_stop $param_cv_p_stop
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103 #end if
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104 #if $param_cv_c_start:
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105 -cv:c_start $param_cv_c_start
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106 #end if
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107 #if $param_cv_c_step_size:
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108 -cv:c_step_size $param_cv_c_step_size
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109 #end if
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110 #if $param_cv_c_stop:
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111 -cv:c_stop $param_cv_c_stop
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112 #end if
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113 #if $param_cv_nu_start:
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114 -cv:nu_start $param_cv_nu_start
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115 #end if
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116 #if $param_cv_nu_step_size:
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117 -cv:nu_step_size $param_cv_nu_step_size
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118 #end if
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119 #if $param_cv_nu_stop:
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120 -cv:nu_stop $param_cv_nu_stop
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121 #end if
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122 #if $param_cv_sigma_start:
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123 -cv:sigma_start $param_cv_sigma_start
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124 #end if
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125 #if $param_cv_sigma_step_size:
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126 -cv:sigma_step_size $param_cv_sigma_step_size
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127 #end if
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128 #if $param_cv_sigma_stop:
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129 -cv:sigma_stop $param_cv_sigma_stop
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130 #end if
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131 #if $adv_opts.adv_opts_selector=='advanced':
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132 #if $adv_opts.param_force:
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133 -force
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134 #end if
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135 #end if
0
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136 </command>
4
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137 <inputs>
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138 <param format="xml,txt" help="(-in) It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line. &lt;br&gt;" label="This is the name of the input file (RT prediction)" name="param_in" optional="True" type="data"/>
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139 <param format="xml" help="(-in_positive) " label="input file with positive examples (peptide separation prediction)" name="param_in_positive" optional="True" type="data"/>
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140 <param format="xml" help="(-in_negative) " label="input file with negative examples (peptide separation prediction)" name="param_in_negative" optional="True" type="data"/>
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141 <param help="(-svm_type) " label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set &lt;br&gt;to C_SVC for separation prediction)" name="param_svm_type" optional="True" type="select" value="NU_SVR">
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142 <option value="NU_SVR">NU_SVR</option>
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143 <option value="NU_SVC">NU_SVC</option>
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144 <option value="EPSILON_SVR">EPSILON_SVR</option>
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145 <option value="C_SVC">C_SVC</option>
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146 </param>
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147 <param help="(-nu) " label="the nu parameter [0..1] of the svm (for nu-SVR)" max="1.0" min="0.0" name="param_nu" optional="True" type="float" value="0.5"/>
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148 <param help="(-p) " label="the epsilon parameter of the svm (for epsilon-SVR)" name="param_p" type="float" value="0.1"/>
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149 <param help="(-c) " label="the penalty parameter of the svm" name="param_c" type="float" value="1.0"/>
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150 <param help="(-kernel_type) " label="the kernel type of the svm" name="param_kernel_type" optional="True" type="select" value="OLIGO">
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151 <option value="LINEAR">LINEAR</option>
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152 <option value="RBF">RBF</option>
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153 <option value="POLY">POLY</option>
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154 <option value="OLIGO">OLIGO</option>
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155 </param>
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156 <param help="(-degree) " label="the degree parameter of the kernel function of the svm (POLY kernel)" min="1" name="param_degree" optional="True" type="integer" value="1"/>
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157 <param help="(-border_length) " label="length of the POBK" min="1" name="param_border_length" optional="True" type="integer" value="22"/>
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158 <param help="(-max_std) " label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" min="0.0" name="param_max_std" optional="True" type="float" value="10.0"/>
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159 <param help="(-k_mer_length) " label="k_mer length of the POBK" min="1" name="param_k_mer_length" optional="True" type="integer" value="1"/>
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160 <param help="(-sigma) " label="sigma of the POBK" name="param_sigma" type="float" value="5.0"/>
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161 <param help="(-total_gradient_time) " label="the time (in seconds) of the gradient (only for RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
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162 <param checked="false" falsevalue="" help="(-first_dim_rt) " label="if set the model will be built for first_dim_rt" name="param_first_dim_rt" optional="True" truevalue="-first_dim_rt" type="boolean"/>
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163 <param checked="false" falsevalue="" help="(-additive_cv) " label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied &lt;br&gt;with the step size to get the new value" name="param_additive_cv" optional="True" truevalue="-additive_cv" type="boolean"/>
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164 <param checked="false" falsevalue="" help="(-skip_cv) " label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" name="param_cv_skip_cv" optional="True" truevalue="-cv:skip_cv" type="boolean"/>
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165 <param help="(-number_of_runs) " label="number of runs for the CV (each run creates a new random partition of the data)" min="1" name="param_cv_number_of_runs" optional="True" type="integer" value="1"/>
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166 <param help="(-number_of_partitions) " label="number of CV partitions" min="2" name="param_cv_number_of_partitions" optional="True" type="integer" value="10"/>
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167 <param help="(-degree_start) " label="starting point of degree" min="1" name="param_cv_degree_start" optional="True" type="integer" value="1"/>
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168 <param help="(-degree_step_size) " label="step size point of degree" name="param_cv_degree_step_size" type="integer" value="2"/>
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169 <param help="(-degree_stop) " label="stopping point of degree" name="param_cv_degree_stop" type="integer" value="4"/>
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170 <param help="(-p_start) " label="starting point of p" name="param_cv_p_start" type="float" value="1.0"/>
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171 <param help="(-p_step_size) " label="step size point of p" name="param_cv_p_step_size" type="float" value="10.0"/>
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172 <param help="(-p_stop) " label="stopping point of p" name="param_cv_p_stop" type="float" value="1000.0"/>
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173 <param help="(-c_start) " label="starting point of c" name="param_cv_c_start" type="float" value="1.0"/>
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174 <param help="(-c_step_size) " label="step size of c" name="param_cv_c_step_size" type="float" value="10.0"/>
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175 <param help="(-c_stop) " label="stopping point of c" name="param_cv_c_stop" type="float" value="1000.0"/>
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176 <param help="(-nu_start) " label="starting point of nu" max="1.0" min="0.0" name="param_cv_nu_start" optional="True" type="float" value="0.3"/>
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177 <param help="(-nu_step_size) " label="step size of nu" name="param_cv_nu_step_size" type="float" value="1.2"/>
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178 <param help="(-nu_stop) " label="stopping point of nu" max="1.0" min="0.0" name="param_cv_nu_stop" optional="True" type="float" value="0.7"/>
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179 <param help="(-sigma_start) " label="starting point of sigma" name="param_cv_sigma_start" type="float" value="1.0"/>
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180 <param help="(-sigma_step_size) " label="step size of sigma" name="param_cv_sigma_step_size" type="float" value="1.3"/>
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181 <param help="(-sigma_stop) " label="stopping point of sigma" name="param_cv_sigma_stop" type="float" value="15.0"/>
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182 <expand macro="advanced_options">
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183 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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184 </expand>
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185 </inputs>
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186 <outputs>
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187 <data format="txt" name="param_out"/>
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188 </outputs>
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189 <help>Trains a model for the retention time prediction of peptides from a training set.
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190
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191
4
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192 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>
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193 </tool>