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annotate ensemble.xml @ 17:760a92d0e174 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
author bgruening
date Mon, 09 Jul 2018 14:27:25 -0400
parents 3c55bac7605a
children 0070e491573f
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31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1 <tool id="sklearn_ensemble" name="Ensemble methods" version="@VERSION@">
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2 <description>for classification and regression</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command><![CDATA[
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10 python "$ensemble_script" '$inputs'
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11 ]]>
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12 </command>
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13 <configfiles>
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14 <inputs name="inputs"/>
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15 <configfile name="ensemble_script">
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16 <![CDATA[
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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17 import sys
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18 import json
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19 import numpy as np
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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20 import sklearn.ensemble
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21 import pandas
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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22 import pickle
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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23 from scipy.io import mmread
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24
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25 @COLUMNS_FUNCTION@
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26 @GET_X_y_FUNCTION@
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27
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28 input_json_path = sys.argv[1]
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29 params = json.load(open(input_json_path, "r"))
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31 #if $selected_tasks.selected_task == "train":
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32
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33 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
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34 options = params["selected_tasks"]["selected_algorithms"]["options"]
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35 if "select_max_features" in options:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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36 if options["select_max_features"]["max_features"] == "number_input":
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37 options["select_max_features"]["max_features"] = options["select_max_features"]["num_max_features"]
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38 options["select_max_features"].pop("num_max_features")
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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39 options["max_features"] = options["select_max_features"]["max_features"]
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40 options.pop("select_max_features")
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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41 if "presort" in options:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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42 if options["presort"] == "true":
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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43 options["presort"] = True
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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44 if options["presort"] == "false":
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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45 options["presort"] = False
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46 if "min_samples_leaf" in options and options["min_samples_leaf"] == 1.0:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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47 options["min_samples_leaf"] = 1
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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48 if "min_samples_split" in options and options["min_samples_split"] > 1.0:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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49 options["min_samples_split"] = int(options["min_samples_split"])
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50
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51 X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2")
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52
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53 my_class = getattr(sklearn.ensemble, algorithm)
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54 estimator = my_class(**options)
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55 estimator.fit(X,y)
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56 pickle.dump(estimator,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL)
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57
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58 #else:
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59 classifier_object = pickle.load(open("$selected_tasks.infile_model", 'r'))
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60 header = 'infer' if params["selected_tasks"]["header"] else None
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61 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
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62 prediction = classifier_object.predict(data)
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63 prediction_df = pandas.DataFrame(prediction)
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64 res = pandas.concat([data, prediction_df], axis=1)
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65 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
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66 #end if
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67
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68 ]]>
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69 </configfile>
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70 </configfiles>
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71 <inputs>
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72 <expand macro="sl_Conditional" model="zip">
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73 <param name="selected_algorithm" type="select" label="Select an ensemble method:">
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74 <option value="RandomForestClassifier" selected="true">Random forest classifier</option>
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75 <option value="AdaBoostClassifier">Ada boost classifier</option>
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76 <option value="GradientBoostingClassifier">Gradient Boosting Classifier</option>
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77 <option value="RandomForestRegressor">Random forest regressor</option>
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78 <option value="AdaBoostRegressor">Ada boost regressor</option>
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79 <option value="GradientBoostingRegressor">Gradient Boosting Regressor</option>
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80 </param>
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81 <when value="RandomForestClassifier">
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82 <expand macro="sl_mixed_input"/>
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83 <section name="options" title="Advanced Options" expanded="False">
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84 <expand macro="n_estimators"/>
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85 <expand macro="criterion"/>
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86 <expand macro="max_features"/>
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87 <expand macro="max_depth"/>
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88 <expand macro="min_samples_split"/>
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89 <expand macro="min_samples_leaf"/>
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90 <expand macro="min_weight_fraction_leaf"/>
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91 <expand macro="max_leaf_nodes"/>
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92 <expand macro="bootstrap"/>
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93 <expand macro="warm_start" checked="false"/>
9
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94 <expand macro="n_jobs"/>
0
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95 <expand macro="random_state"/>
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96 <expand macro="oob_score"/>
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97 <!--class_weight=None-->
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98 </section>
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99 </when>
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100 <when value="AdaBoostClassifier">
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101 <expand macro="sl_mixed_input"/>
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102 <section name="options" title="Advanced Options" expanded="False">
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103 <!--base_estimator=None-->
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104 <expand macro="n_estimators" default_value="50"/>
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105 <expand macro="learning_rate"/>
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106 <param argument="algorithm" type="select" label="Boosting algorithm" help=" ">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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107 <option value="SAMME.R" selected="true">SAMME.R</option>
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108 <option value="SAMME">SAMME</option>
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109 </param>
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110 <expand macro="random_state"/>
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111 </section>
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112 </when>
9
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113 <when value="GradientBoostingClassifier">
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114 <expand macro="sl_mixed_input"/>
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115 <section name="options" title="Advanced Options" expanded="False">
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116 <!--base_estimator=None-->
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117 <param argument="loss" type="select" label="Loss function">
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118 <option value="deviance" selected="true">deviance - logistic regression with probabilistic outputs</option>
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119 <option value="exponential">exponential - gradient boosting recovers the AdaBoost algorithm</option>
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120 </param>
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121 <expand macro="learning_rate" default_value='0.1'/>
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122 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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123 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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124 <expand macro="criterion2">
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125 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
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126 </expand>
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127 <expand macro="min_samples_split" type="float"/>
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128 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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129 <expand macro="min_weight_fraction_leaf"/>
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130 <expand macro="subsample"/>
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131 <expand macro="max_features"/>
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132 <expand macro="max_leaf_nodes"/>
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133 <expand macro="min_impurity_decrease"/>
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134 <expand macro="verbose"/>
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135 <expand macro="warm_start" checked="false"/>
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136 <expand macro="random_state"/>
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137 <expand macro="presort"/>
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138 </section>
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139 </when>
0
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140 <when value="RandomForestRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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141 <expand macro="sl_mixed_input"/>
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142 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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143 <expand macro="n_estimators"/>
9
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144 <expand macro="criterion2"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
145 <expand macro="max_features"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
146 <expand macro="max_depth"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
147 <expand macro="min_samples_split"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
148 <expand macro="min_samples_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
149 <expand macro="min_weight_fraction_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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150 <expand macro="max_leaf_nodes"/>
9
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diff changeset
151 <expand macro="min_impurity_decrease"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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152 <expand macro="bootstrap"/>
9
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diff changeset
153 <expand macro="oob_score"/>
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diff changeset
154 <expand macro="n_jobs"/>
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diff changeset
155 <expand macro="random_state"/>
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156 <expand macro="verbose"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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157 <expand macro="warm_start" checked="false"/>
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158 </section>
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159 </when>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
160 <when value="AdaBoostRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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161 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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162 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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163 <!--base_estimator=None-->
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164 <expand macro="n_estimators" default_value="50"/>
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165 <expand macro="learning_rate"/>
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166 <param argument="loss" type="select" label="Loss function" optional="true" help="Used when updating the weights after each boosting iteration. ">
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167 <option value="linear" selected="true">linear</option>
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168 <option value="square">square</option>
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169 <option value="exponential">exponential</option>
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170 </param>
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171 <expand macro="random_state"/>
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172 </section>
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173 </when>
9
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174 <when value="GradientBoostingRegressor">
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175 <expand macro="sl_mixed_input"/>
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176 <section name="options" title="Advanced Options" expanded="False">
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177 <param argument="loss" type="select" label="Loss function">
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178 <option value="ls" selected="true">ls - least squares regression</option>
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179 <option value="lad">lad - least absolute deviation</option>
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180 <option value="huber">huber - combination of least squares regression and least absolute deviation</option>
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181 <option value="quantile">quantile - use alpha to specify the quantile</option>
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182 </param>
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diff changeset
183 <expand macro="learning_rate" default_value="0.1"/>
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184 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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185 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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186 <expand macro="criterion2">
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187 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
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188 </expand>
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189 <expand macro="min_samples_split" type="float"/>
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190 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node"/>
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191 <expand macro="min_weight_fraction_leaf"/>
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192 <expand macro="subsample"/>
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193 <expand macro="max_features"/>
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194 <expand macro="max_leaf_nodes"/>
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195 <expand macro="min_impurity_decrease"/>
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196 <param argument="alpha" type="float" value="0.9" label="alpha" help="The alpha-quantile of the huber loss function and the quantile loss function" />
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197 <!--base_estimator=None-->
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198 <expand macro="verbose"/>
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199 <expand macro="warm_start" checked="false"/>
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200 <expand macro="random_state"/>
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201 <expand macro="presort"/>
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202 </section>
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203 </when>
0
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204 </expand>
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205 </inputs>
4
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206
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207 <expand macro="output"/>
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208
0
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209 <tests>
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210 <test>
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211 <param name="infile1" value="train.tabular" ftype="tabular"/>
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212 <param name="infile2" value="train.tabular" ftype="tabular"/>
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213 <param name="col1" value="1,2,3,4"/>
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214 <param name="col2" value="5"/>
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215 <param name="selected_task" value="train"/>
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216 <param name="selected_algorithm" value="RandomForestClassifier"/>
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217 <param name="random_state" value="10"/>
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218 <output name="outfile_fit" file="rfc_model01" compare="sim_size" delta="500"/>
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219 </test>
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220 <test>
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221 <param name="infile_model" value="rfc_model01" ftype="zip"/>
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222 <param name="infile_data" value="test.tabular" ftype="tabular"/>
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223 <param name="selected_task" value="load"/>
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224 <output name="outfile_predict" file="rfc_result01" compare="sim_size" delta="500"/>
0
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225 </test>
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226 <test>
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227 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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228 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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229 <param name="col1" value="1,2,3,4,5"/>
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230 <param name="col2" value="6"/>
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231 <param name="selected_task" value="train"/>
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232 <param name="selected_algorithm" value="RandomForestRegressor"/>
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233 <param name="random_state" value="10"/>
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234 <output name="outfile_fit" file="rfr_model01" compare="sim_size" delta="500"/>
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235 </test>
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236 <test>
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237 <param name="infile_model" value="rfr_model01" ftype="zip"/>
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238 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/>
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239 <param name="selected_task" value="load"/>
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240 <output name="outfile_predict" file="rfr_result01" compare="sim_size" delta="500"/>
0
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241 </test>
9
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242 <test>
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243 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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244 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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245 <param name="header1" value="True"/>
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246 <param name="selected_column_selector_option" value="all_columns"/>
9
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247 <param name="header2" value="True"/>
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248 <param name="col2" value="1"/>
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249 <param name="selected_task" value="train"/>
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250 <param name="selected_algorithm" value="GradientBoostingRegressor"/>
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251 <param name="max_features" value="number_input"/>
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252 <param name="num_max_features" value=""/>
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253 <param name="random_state" value="42"/>
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254 <output name="outfile_fit" file="gbr_model01" compare="sim_size" delta="500"/>
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255 </test>
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256 <test>
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257 <param name="infile_model" value="gbr_model01" ftype="zip"/>
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258 <param name="infile_data" value="regression_test_X.tabular" ftype="tabular"/>
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259 <param name="selected_task" value="load"/>
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260 <param name="header" value="True"/>
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261 <output name="outfile_predict" file="gbr_prediction_result01.tabular" compare="sim_size" delta="500"/>
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262 </test>
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263 <test>
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264 <param name="infile1" value="train.tabular" ftype="tabular"/>
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265 <param name="infile2" value="train.tabular" ftype="tabular"/>
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266 <param name="col1" value="1,2,3,4"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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267 <param name="col2" value="5"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
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268 <param name="selected_task" value="train"/>
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269 <param name="selected_algorithm" value="GradientBoostingClassifier"/>
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270 <output name="outfile_fit" file="gbc_model01" compare="sim_size" delta="500"/>
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271 </test>
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272 <test>
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273 <param name="infile_model" value="gbc_model01" ftype="zip"/>
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274 <param name="infile_data" value="test.tabular" ftype="tabular"/>
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275 <param name="selected_task" value="load"/>
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276 <output name="outfile_predict" file="gbc_result01" compare="sim_size" delta="500"/>
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277 </test>
0
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278 </tests>
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279 <help><![CDATA[
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280 ***What it does***
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281 The goal of ensemble methods is to combine the predictions of several base estimators built with a given learning algorithm in order to improve generalizability / robustness over a single estimator. This tool offers two sets of ensemble algorithms for classification and regression: random forests and ADA boosting which are based on sklearn.ensemble library from Scikit-learn. Here you can find out about the input, output and methods presented in the tools. For information about ensemble methods and parameters settings please refer to `Scikit-learn ensemble`_.
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282
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283 .. _`Scikit-learn ensemble`: http://scikit-learn.org/stable/modules/ensemble.html
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284
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285 **1 - Methods**
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286 There are two groups of operations available:
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287
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288 1 - Train a model : A training set containing samples and their respective labels (or predicted values) are input. Based on the selected algorithm and options, an estimator object is fit to the data and is returned.
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289
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290 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset.
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291
0
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292 **2 - Trainig input**
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293 When you choose to train a model, you need a features dataset X and a labels set y. This tool expects tabular or sparse data for X and a single column for y (tabular). You can select a subset of columns in a tabular dataset as your features dataset or labels column. Below you find some examples:
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294
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295 **Sample tabular features dataset**
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296 The following training dataset contains 3 feature columns and a column containing class labels. You can simply select the first 3 columns as features and the last column as labels:
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297
0
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298 ::
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299
0
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300 4.01163365529 -6.10797684314 8.29829894763 1
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301 10.0788438916 1.59539821454 10.0684278289 0
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302 -5.17607775503 -0.878286135332 6.92941850665 2
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303 4.00975406235 -7.11847496542 9.3802423585 1
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304 4.61204065139 -5.71217537352 9.12509610964 1
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305
0
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306
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307 **Sample sparse features dataset**
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308 In this case you cannot specifiy a column range.
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309
0
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310 ::
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311
0
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312 4 1048577 8738
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313 1 271 0.02083333333333341
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314 1 1038 0.02461995616119806
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315 2 829017 0.01629088031127686
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316 2 829437 0.01209127083516686
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317 2 830752 0.02535100632816968
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318 3 1047487 0.01485722929945572
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319 3 1047980 0.02640566620767753
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320 3 1048475 0.01665869913262564
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321 4 608 0.01662975263094352
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322 4 1651 0.02519674277562741
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323 4 4053 0.04223659971350601
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324
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325
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326 **2 - Trainig output**
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327 The trained model is generated and output in the form of a binary file.
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328
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329
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330 **3 - Prediction input**
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331
0
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332 When you choose to load a model and do prediction, the tool expects an already trained estimator and a tabular dataset as input. The dataset contains new samples which you want to classify or predict regression values for.
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333
0
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334
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335 .. class:: warningmark
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336
0
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337 The number of feature columns must be the same in training and prediction datasets!
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338
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339
0
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340 **3 - Prediction output**
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341 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset.
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342
0
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343 ]]></help>
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344 <expand macro="sklearn_citation"/>
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345 </tool>