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annotate svm.xml @ 12:ada7bb28fe13 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
author bgruening
date Sun, 01 Jul 2018 03:18:53 -0400
parents 9a9396e5d153
children 78c664cc1841
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9a9396e5d153 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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1 <tool id="svm_classifier" name="Support vector machines (SVMs)" version="@VERSION@">
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2 <description>for classification</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 <!-- macro name="class_weight" argument="class_weight"-->
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6 </macros>
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7 <expand macro="python_requirements"/>
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8 <expand macro="macro_stdio"/>
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command><![CDATA[
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11 python "$svc_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs"/>
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16 <configfile name="svc_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import numpy as np
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21 import sklearn.svm
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22 import pandas
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23 import pickle
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25 input_json_path = sys.argv[1]
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26 params = json.load(open(input_json_path, "r"))
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28 #if $selected_tasks.selected_task == "load":
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30 classifier_object = pickle.load(open("$infile_model", 'rb'))
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32 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
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33 prediction = classifier_object.predict(data)
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34 prediction_df = pandas.DataFrame(prediction)
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35 res = pandas.concat([data, prediction_df], axis=1)
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36 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
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38 #else:
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40 data_train = pandas.read_csv("$selected_tasks.infile_train", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
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42 data = data_train.ix[:,0:len(data_train.columns)-1]
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43 labels = np.array(data_train[data_train.columns[len(data_train.columns)-1]])
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45 options = params["selected_tasks"]["selected_algorithms"]["options"]
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46 selected_algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
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48 if not(selected_algorithm=="LinearSVC"):
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49 if options["kernel"]:
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50 options["kernel"] = str(options["kernel"])
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52 my_class = getattr(sklearn.svm, selected_algorithm)
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53 classifier_object = my_class(**options)
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54 classifier_object.fit(data,labels)
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56 pickle.dump(classifier_object,open("$outfile_fit", 'w+'))
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57
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58 #end if
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60 ]]>
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61 </configfile>
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62 </configfiles>
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63 <inputs>
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64 <expand macro="train_loadConditional" model="zip">
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65 <param name="selected_algorithm" type="select" label="Classifier type">
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66 <option value="SVC">C-Support Vector Classification</option>
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67 <option value="NuSVC">Nu-Support Vector Classification</option>
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68 <option value="LinearSVC">Linear Support Vector Classification</option>
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69 </param>
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70 <when value="SVC">
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71 <expand macro="svc_advanced_options">
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72 <expand macro="C"/>
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73 </expand>
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74 </when>
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75 <when value="NuSVC">
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76 <expand macro="svc_advanced_options">
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77 <param argument="nu" type="float" optional="true" value="0.5" label="Nu control parameter" help="Controls the number of support vectors. Should be in the interval (0, 1]. "/>
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78 </expand>
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79 </when>
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80 <when value="LinearSVC">
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81 <section name="options" title="Advanced Options" expanded="False">
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82 <expand macro="C"/>
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83 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
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84 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
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85 <!--expand macro="class_weight"/-->
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86 <param argument="max_iter" type="integer" optional="true" value="1000" label="Maximum number of iterations" help="The maximum number of iterations to be run."/>
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87 <param argument="loss" type="select" label="Loss function" help="Specifies the loss function. ''squared_hinge'' is the square of the hinge loss.">
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88 <option value="squared_hinge" selected="true">Squared hinge</option>
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89 <option value="hinge">Hinge</option>
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90 </param>
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91 <param argument="penalty" type="select" label="Penalization norm" help=" ">
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92 <option value="l1" >l1</option>
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93 <option value="l2" selected="true">l2</option>
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94 </param>
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95 <param argument="dual" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help="Select the algorithm to either solve the dual or primal optimization problem. Prefer dual=False when n_samples > n_features."/>
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96 <param argument="multi_class" type="select" label="Multi-class strategy" help="Determines the multi-class strategy if y contains more than two classes.">
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97 <option value="ovr" selected="true">ovr</option>
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98 <option value="crammer_singer" >crammer_singer</option>
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99 </param>
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100 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Calculate the intercept for this model" help="If set to false, data is expected to be already centered."/>
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101 <param argument="intercept_scaling" type="float" optional="true" value="1" label="Add synthetic feature to the instance vector" help=" "/>
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102 </section>
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103 </when>
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104 </expand>
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105 </inputs>
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106
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107 <expand macro="output"/>
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108
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109 <tests>
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110 <test>
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111 <param name="infile_train" value="train_set.tabular" ftype="tabular"/>
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112 <param name="selected_task" value="train"/>
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113 <param name="selected_algorithm" value="SVC"/>
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114 <param name="random_state" value="5"/>
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115 <output name="outfile_fit" file="svc_model01.txt"/>
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116 </test>
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117 <test>
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118 <param name="infile_train" value="train_set.tabular" ftype="tabular"/>
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119 <param name="selected_task" value="train"/>
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120 <param name="selected_algorithm" value="NuSVC"/>
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121 <param name="random_state" value="5"/>
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122 <output name="outfile_fit" file="svc_model02.txt"/>
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123 </test>
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124 <test>
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125 <param name="infile_train" value="train_set.tabular" ftype="tabular"/>
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126 <param name="selected_task" value="train"/>
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127 <param name="selected_algorithm" value="LinearSVC"/>
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128 <param name="random_state" value="5"/>
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129 <output name="outfile_fit" file="svc_model03.txt"/>
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130 </test>
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131 <test>
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132 <param name="infile_model" value="svc_model01.txt" ftype="txt"/>
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133 <param name="infile_data" value="test_set.tabular" ftype="tabular"/>
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134 <param name="selected_task" value="load"/>
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135 <output name="outfile_predict" file="svc_prediction_result01.tabular"/>
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136 </test>
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137 <test>
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138 <param name="infile_model" value="svc_model02.txt" ftype="txt"/>
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139 <param name="infile_data" value="test_set.tabular" ftype="tabular"/>
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140 <param name="selected_task" value="load"/>
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141 <output name="outfile_predict" file="svc_prediction_result02.tabular"/>
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142 </test>
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143 <test>
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144 <param name="infile_model" value="svc_model03.txt" ftype="txt"/>
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145 <param name="infile_data" value="test_set.tabular" ftype="tabular"/>
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146 <param name="selected_task" value="load"/>
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147 <output name="outfile_predict" file="svc_prediction_result03.tabular"/>
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 **What it does**
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152 This module implements the Support Vector Machine (SVM) classification algorithms.
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153 Support vector machines (SVMs) are a set of supervised learning methods used for classification, regression and outliers detection.
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154
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155 **The advantages of support vector machines are:**
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156
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157 1- Effective in high dimensional spaces.
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158
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159 2- Still effective in cases where number of dimensions is greater than the number of samples.
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160
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161 3- Uses a subset of training points in the decision function (called support vectors), so it is also memory efficient.
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162
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163 4- Versatile: different Kernel functions can be specified for the decision function. Common kernels are provided, but it is also possible to specify custom kernels.
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164
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165 **The disadvantages of support vector machines include:**
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166
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167 1- If the number of features is much greater than the number of samples, the method is likely to give poor performances.
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168
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169 2- SVMs do not directly provide probability estimates, these are calculated using an expensive five-fold cross-validation
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170
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171 For more information check http://scikit-learn.org/stable/modules/neighbors.html
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172
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173 ]]>
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174 </help>
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175 <expand macro="sklearn_citation"/>
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176 </tool>