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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RTModel" name="RTModel" version="1.12.0">
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3 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">RTModel</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>RTModel
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11
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12 -in ${param_in}
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13 -in_positive ${param_in_positive}
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14 -in_negative ${param_in_negative}
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15 -out ${param_out}
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16 -svm_type ${param_svm_type}
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17 -nu ${param_nu}
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18 -p ${param_p}
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19 -c ${param_c}
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20 -kernel_type ${param_kernel_type}
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21 -degree ${param_degree}
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22 -border_length ${param_border_length}
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23 -max_std ${param_max_std}
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24 -k_mer_length ${param_k_mer_length}
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25 -sigma ${param_sigma}
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26 -total_gradient_time ${param_total_gradient_time}
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27 ${param_first_dim_rt}
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28 ${param_additive_cv}
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29 -threads \${GALAXY_SLOTS:-24}
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30 ${param_skip_cv}
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31 -cv:number_of_runs ${param_number_of_runs}
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32 -cv:number_of_partitions ${param_number_of_partitions}
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33 -cv:degree_start ${param_degree_start}
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34 -cv:degree_step_size ${param_degree_step_size}
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35 -cv:degree_stop ${param_degree_stop}
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36 -cv:p_start ${param_p_start}
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37 -cv:p_step_size ${param_p_step_size}
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38 -cv:p_stop ${param_p_stop}
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39 -cv:c_start ${param_c_start}
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40 -cv:c_step_size ${param_c_step_size}
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41 -cv:c_stop ${param_c_stop}
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42 -cv:nu_start ${param_nu_start}
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43 -cv:nu_step_size ${param_nu_step_size}
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44 -cv:nu_stop ${param_nu_stop}
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45 -cv:sigma_start ${param_sigma_start}
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46 -cv:sigma_step_size ${param_sigma_step_size}
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47 -cv:sigma_stop ${param_sigma_stop}
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48 </command>
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49 <inputs>
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50 <param name="param_in" type="data" format="idXML,txt" optional="True" label="This is the name of the input file (RT prediction). 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.#br#" help="(-in)"/>
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51 <param name="param_in_positive" type="data" format="idXML" optional="True" label="input file with positive examples (peptide separation prediction)#br#" help="(-in_positive)"/>
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52 <param name="param_in_negative" type="data" format="idXML" optional="True" label="input file with negative examples (peptide separation prediction)#br#" help="(-in_negative)"/>
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53 <param name="param_svm_type" type="select" optional="True" value="NU_SVR" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set#br#to C_SVC for separation prediction)#br#" help="(-svm_type)">
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54 <option value="NU_SVR">NU_SVR</option>
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55 <option value="NU_SVC">NU_SVC</option>
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56 <option value="EPSILON_SVR">EPSILON_SVR</option>
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57 <option value="C_SVC">C_SVC</option>
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58 </param>
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59 <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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60 <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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61 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c)"/>
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62 <param name="param_kernel_type" type="select" optional="True" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type)">
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63 <option value="LINEAR">LINEAR</option>
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64 <option value="RBF">RBF</option>
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65 <option value="POLY">POLY</option>
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66 <option value="OLIGO">OLIGO</option>
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67 </param>
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68 <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)#br#" help="(-degree)"/>
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69 <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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70 <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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71 <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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72 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma)"/>
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73 <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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74 <param name="param_first_dim_rt" type="boolean" truevalue="-first_dim_rt true" falsevalue="-first_dim_rt false" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt)"/>
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75 <param name="param_additive_cv" type="boolean" truevalue="-additive_cv true" falsevalue="-additive_cv false" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied#br#with the step size to get the new value" help="(-additive_cv)"/>
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76 <param name="param_skip_cv" type="boolean" truevalue="-cv:skip_cv true" falsevalue="-cv:skip_cv false" 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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77 <param name="param_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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78 <param name="param_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions)"/>
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79 <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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80 <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
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81 <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
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82 <param name="param_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start)"/>
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83 <param name="param_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size)"/>
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84 <param name="param_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop)"/>
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85 <param name="param_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start)"/>
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86 <param name="param_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size)"/>
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87 <param name="param_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop)"/>
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88 <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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89 <param name="param_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size)"/>
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90 <param name="param_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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91 <param name="param_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start)"/>
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92 <param name="param_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size)"/>
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93 <param name="param_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop)"/>
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94 </inputs>
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95 <outputs>
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96 <data name="param_out" label="output file: the model in libsvm format" format="txt"/>
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97 </outputs>
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98 <help>**What it does**
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99
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100 Trains a model for the retention time prediction of peptides from a training set.
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101
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102
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103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html
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104
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105 @REFERENCES@
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106 </help>
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107 </tool>
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