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annotate ensemble.xml @ 6:4c2fae2db5d1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
author bgruening
date Tue, 13 Mar 2018 04:51:40 -0400
parents 3bc536788043
children ea8b1c89c20b
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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
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20 import sklearn.ensemble
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21 import pandas
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22 import pickle
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23 from scipy.io import mmread
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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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27
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28 @COLUMNS_FUNCTION@
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29
0
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30 #if $selected_tasks.selected_task == "train":
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31
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32 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
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33 options = params["selected_tasks"]["selected_algorithms"]["options"]
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34 input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"]
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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35 if input_type=="tabular":
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36 X = read_columns(
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37 "$selected_tasks.selected_algorithms.input_options.infile1",
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38 "$selected_tasks.selected_algorithms.input_options.col1",
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39 sep='\t',
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40 header=None,
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41 parse_dates=True
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42 )
0
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43 else:
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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44 X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r'))
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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45
6
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46 y = read_columns(
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47 "$selected_tasks.selected_algorithms.input_options.infile2",
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48 "$selected_tasks.selected_algorithms.input_options.col2",
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49 sep='\t',
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50 header=None,
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51 parse_dates=True
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52 )
0
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53
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54 my_class = getattr(sklearn.ensemble, algorithm)
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55 estimator = my_class(**options)
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56 estimator.fit(X,y)
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57 pickle.dump(estimator,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL)
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58
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59 #else:
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60 classifier_object = pickle.load(open("$selected_tasks.infile_model", 'r'))
6
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61 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
0
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62 prediction = classifier_object.predict(data)
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63 prediction_df = pandas.DataFrame(prediction)
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64 res = pandas.concat([data, prediction_df], axis=1)
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65 res.to_csv(path_or_buf = "$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="RandomForestRegressor">Random forest regressor</option>
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77 <option value="AdaBoostRegressor">Ada boost regressor</option>
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78 </param>
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79 <when value="RandomForestClassifier">
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80 <expand macro="sl_mixed_input"/>
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81 <section name="options" title="Advanced Options" expanded="False">
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82 <expand macro="n_estimators"/>
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83 <expand macro="criterion"/>
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84 <expand macro="max_features"/>
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85 <expand macro="max_depth"/>
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86 <expand macro="min_samples_split"/>
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87 <expand macro="min_samples_leaf"/>
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88 <expand macro="min_weight_fraction_leaf"/>
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89 <expand macro="max_leaf_nodes"/>
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90 <expand macro="bootstrap"/>
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91 <expand macro="warm_start" checked="false"/>
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92 <expand macro="random_state"/>
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93 <expand macro="oob_score"/>
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94 <!--class_weight=None-->
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95 </section>
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96 </when>
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97 <when value="AdaBoostClassifier">
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98 <expand macro="sl_mixed_input"/>
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99 <section name="options" title="Advanced Options" expanded="False">
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100 <!--base_estimator=None-->
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101 <expand macro="n_estimators" default_value="50"/>
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102 <expand macro="learning_rate"/>
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103 <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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104 <option value="SAMME.R" selected="true">SAMME.R</option>
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105 <option value="SAMME">SAMME</option>
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106 </param>
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107 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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108 </section>
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109 </when>
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110 <when value="RandomForestRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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111 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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112 <section name="options" title="Advanced Options" expanded="False">
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113 <expand macro="n_estimators"/>
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114 <expand macro="max_features"/>
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115 <expand macro="max_depth"/>
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116 <expand macro="min_samples_split"/>
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117 <expand macro="min_samples_leaf"/>
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118 <expand macro="min_weight_fraction_leaf"/>
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119 <expand macro="max_leaf_nodes"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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120 <expand macro="bootstrap"/>
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121 <expand macro="warm_start" checked="false"/>
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122 <expand macro="random_state"/>
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123 <expand macro="oob_score"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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124 </section>
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125 </when>
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126 <when value="AdaBoostRegressor">
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127 <expand macro="sl_mixed_input"/>
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128 <section name="options" title="Advanced Options" expanded="False">
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129 <!--base_estimator=None-->
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130 <expand macro="n_estimators" default_value="50"/>
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131 <expand macro="learning_rate"/>
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132 <param argument="loss" type="select" label="Loss function" optional="true" help="Used when updating the weights after each boosting iteration. ">
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133 <option value="linear" selected="true">linear</option>
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134 <option value="square">square</option>
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135 <option value="exponential">exponential</option>
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136 </param>
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137 <expand macro="random_state"/>
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138 </section>
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139 </when>
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140 </expand>
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141 </inputs>
4
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142
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143 <expand macro="output"/>
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144
0
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145 <tests>
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146 <test>
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147 <param name="infile1" value="train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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148 <param name="infile2" value="train.tabular" ftype="tabular"/>
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149 <param name="col1" value="1,2,3,4"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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150 <param name="col2" value="5"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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151 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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152 <param name="selected_algorithm" value="RandomForestClassifier"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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153 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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154 <output name="outfile_fit" file="rfc_model01" compare="sim_size" delta="500"/>
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155 </test>
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156 <test>
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157 <param name="infile_model" value="rfc_model01" ftype="zip"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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158 <param name="infile_data" value="test.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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159 <param name="selected_task" value="load"/>
4
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160 <output name="outfile_predict" file="rfc_result01" compare="sim_size" delta="500"/>
0
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161 </test>
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162
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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163 <test>
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164 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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165 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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166 <param name="col1" value="1,2,3,4,5"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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167 <param name="col2" value="6"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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168 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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169 <param name="selected_algorithm" value="RandomForestRegressor"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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170 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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171 <output name="outfile_fit" file="rfr_model01" compare="sim_size" delta="500"/>
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172 </test>
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173 <test>
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174 <param name="infile_model" value="rfr_model01" ftype="zip"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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175 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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176 <param name="selected_task" value="load"/>
4
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177 <output name="outfile_predict" file="rfr_result01" compare="sim_size" delta="500"/>
0
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178 </test>
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179 </tests>
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180 <help><![CDATA[
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181 ***What it does***
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182 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`_.
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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183
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184 .. _`Scikit-learn ensemble`: http://scikit-learn.org/stable/modules/ensemble.html
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185
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186 **1 - Methods**
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187 There are two groups of operations available:
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188
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189 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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190
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191 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset.
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192
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193 **2 - Trainig input**
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194 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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195
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196 **Sample tabular features dataset**
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197 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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198
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199 ::
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200
0
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201 4.01163365529 -6.10797684314 8.29829894763 1
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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202 10.0788438916 1.59539821454 10.0684278289 0
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203 -5.17607775503 -0.878286135332 6.92941850665 2
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204 4.00975406235 -7.11847496542 9.3802423585 1
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205 4.61204065139 -5.71217537352 9.12509610964 1
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206
0
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207
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208 **Sample sparse features dataset**
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209 In this case you cannot specifiy a column range.
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210
0
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211 ::
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212
0
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213 4 1048577 8738
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214 1 271 0.02083333333333341
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215 1 1038 0.02461995616119806
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216 2 829017 0.01629088031127686
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217 2 829437 0.01209127083516686
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218 2 830752 0.02535100632816968
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219 3 1047487 0.01485722929945572
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220 3 1047980 0.02640566620767753
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221 3 1048475 0.01665869913262564
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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222 4 608 0.01662975263094352
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223 4 1651 0.02519674277562741
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224 4 4053 0.04223659971350601
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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225
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226
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227 **2 - Trainig output**
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228 The trained model is generated and output in the form of a binary file.
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229
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230
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231 **3 - Prediction input**
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232
0
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233 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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234
0
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235
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236 .. class:: warningmark
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237
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238 The number of feature columns must be the same in training and prediction datasets!
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240
0
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241 **3 - Prediction output**
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242 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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243
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244 ]]></help>
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245 <expand macro="sklearn_citation"/>
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246 </tool>