Mercurial > repos > bgruening > sklearn_build_pipeline

annotate pipeline.xml @ 13:a528ad09062a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
author bgruening
date Fri, 01 Nov 2019 16:57:35 -0400
parents 0c2586a48d0f
children a7a047cf36d8
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@">
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2 <description>constructs a list of transforms and a final estimator</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>
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10 <![CDATA[
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11 python "$sklearn_pipeline_script" '$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="sklearn_pipeline_script">
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17 <![CDATA[
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18 import imblearn
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19 import json
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20 import pandas as pd
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21 import pickle
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22 import pprint
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23 import skrebate
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24 import sys
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25 import warnings
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26 from sklearn import (
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27 cluster, compose, decomposition, ensemble, feature_extraction,
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28 feature_selection, gaussian_process, kernel_approximation, metrics,
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29 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
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30 svm, linear_model, tree, discriminant_analysis)
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31 from sklearn.pipeline import make_pipeline
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32 from imblearn.pipeline import make_pipeline as imb_make_pipeline
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33 from galaxy_ml.utils import (SafeEval, feature_selector, get_estimator,
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34 try_get_attr, get_search_params)
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37 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
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39 warnings.filterwarnings('ignore')
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41 safe_eval = SafeEval()
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43 input_json_path = sys.argv[1]
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44 with open(input_json_path, 'r') as param_handler:
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45 params = json.load(param_handler)
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46
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47 #if $final_estimator.estimator_selector.selected_module == 'custom_estimator':
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48 params['final_estimator']['estimator_selector']['c_estimator'] =\
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49 '$final_estimator.estimator_selector.c_estimator'
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50 #end if
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51
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52 #if $final_estimator.estimator_selector.selected_module == 'binarize_target':
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53 params['final_estimator']['estimator_selector']['wrapped_estimator'] =\
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54 '$final_estimator.estimator_selector.wrapped_estimator'
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55 #end if
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56
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57 pipeline_steps = []
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58
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59 def get_component(input_json, check_none=False):
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60 is_imblearn = False
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61 if input_json['component_type'] == 'None':
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62 if not check_none:
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63 return None, False
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64 else:
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65 sys.exit("The pre-processing component type can't be None "
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66 "when the number of components is greater than 1.")
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67 if input_json['component_type'] == 'pre_processor':
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68 preprocessor = input_json['pre_processors']['selected_pre_processor']
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69 pre_processor_options = input_json['pre_processors']['options']
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70 if 'feature_range' in pre_processor_options:
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71 feature_range = safe_eval(pre_processor_options['feature_range'].strip())
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72 if not feature_range:
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73 feature_range = (0, 1)
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74 pre_processor_options['feature_range'] = feature_range
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75 my_class = getattr(preprocessing, preprocessor)
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76 obj = my_class(**pre_processor_options)
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77 elif input_json['component_type'] == 'feature_selection':
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78 obj = feature_selector(input_json['fs_algorithm_selector'])
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79 elif input_json['component_type'] == 'decomposition':
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80 algorithm = input_json['matrix_decomposition_selector']['select_algorithm']
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81 obj = getattr(decomposition, algorithm)()
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82 options = input_json['matrix_decomposition_selector']['text_params'].strip()
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83 if options != '':
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84 options = safe_eval( 'dict(' + options + ')' )
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85 obj.set_params(**options)
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86 elif input_json['component_type'] == 'kernel_approximation':
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87 algorithm = input_json['kernel_approximation_selector']['select_algorithm']
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88 obj = getattr(kernel_approximation, algorithm)()
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89 options = input_json['kernel_approximation_selector']['text_params'].strip()
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90 if options != '':
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91 options = safe_eval( 'dict(' + options + ')' )
0
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92 obj.set_params(**options)
3
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93 elif input_json['component_type'] == 'FeatureAgglomeration':
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94 algorithm = input_json['FeatureAgglomeration_selector']['select_algorithm']
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95 obj = getattr(cluster, algorithm)()
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96 options = input_json['FeatureAgglomeration_selector']['text_params'].strip()
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97 if options != '':
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98 options = safe_eval( 'dict(' + options + ')' )
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99 obj.set_params(**options)
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100 elif input_json['component_type'] == 'skrebate':
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101 algorithm = input_json['skrebate_selector']['select_algorithm']
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102 if algorithm == 'TuRF':
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103 obj = getattr(skrebate, algorithm)(core_algorithm='ReliefF')
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104 else:
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105 obj = getattr(skrebate, algorithm)()
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106 options = input_json['skrebate_selector']['text_params'].strip()
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107 if options != '':
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108 options = safe_eval( 'dict(' + options + ')' )
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109 obj.set_params(**options)
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110 elif input_json['component_type'] == 'imblearn':
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111 is_imblearn = True
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112 algorithm = input_json['imblearn_selector']['select_algorithm']
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113 if algorithm == 'over_sampling.SMOTENC':
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114 obj = over_sampling.SMOTENC(categorical_features=[])
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115 elif algorithm == 'Z_RandomOverSampler':
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116 Z_RandomOverSampler = try_get_attr('galaxy_ml.preprocessors',
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117 'Z_RandomOverSampler')
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118 obj = Z_RandomOverSampler()
7
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119 else:
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120 globals = algorithm.split('.')
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121 mod, klass = globals[0], globals[1]
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122 obj = getattr(getattr(imblearn, mod), klass)()
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123 options = input_json['imblearn_selector']['text_params'].strip()
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124 if options != '':
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125 options = safe_eval( 'dict(' + options + ')' )
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126 obj.set_params(**options)
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127 elif input_json['component_type'] == 'IRAPS':
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128 iraps_core = try_get_attr('galaxy_ml.iraps_classifier','IRAPSCore')()
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129 core_params = input_json['text_params'].strip()
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130 if core_params != '':
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131 try:
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132 params = safe_eval('dict(' + core_params + ')')
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133 except ValueError:
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134 sys.exit("Unsupported parameter input: `%s`" % core_params)
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135 iraps_core.set_params(**params)
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136 options = {}
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137 if input_json['p_thres'] is not None:
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138 options['p_thres'] = input_json['p_thres']
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139 if input_json['fc_thres'] is not None:
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140 options['fc_thres'] = input_json['fc_thres']
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141 if input_json['occurrence'] is not None:
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142 options['occurrence'] = input_json['occurrence']
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143 if input_json['discretize'] is not None:
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144 options['discretize'] = input_json['discretize']
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145 IRAPSClassifier = try_get_attr('galaxy_ml.iraps_classifier','IRAPSClassifier')
8
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146 obj = IRAPSClassifier(iraps_core, **options)
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147 elif input_json['component_type'] == 'preprocessors':
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148 encoder_selection = input_json['encoder_selection']
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149 encoder_type = encoder_selection.pop('encoder_type')
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150 klass = try_get_attr('galaxy_ml.preprocessors', encoder_type)
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151 obj = klass(**encoder_selection)
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152
3
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153 if 'n_jobs' in obj.get_params():
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154 obj.set_params( n_jobs=N_JOBS )
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155 return obj, is_imblearn
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156
7
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157 has_imblearn = False
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158 if len(params['pipeline_component']) == 1:
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159 step_obj, is_imblearn = get_component( params['pipeline_component'][0]['component_selector'])
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160 if step_obj:
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diff changeset
161 pipeline_steps.append( step_obj )
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162 if is_imblearn:
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163 has_imblearn = True
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164 else:
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165 for i, c in enumerate(params['pipeline_component']):
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166 step_obj, is_imblearn = get_component( c['component_selector'], check_none=True )
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167 pipeline_steps.append( step_obj )
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168 if is_imblearn:
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169 has_imblearn = True
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170
8
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171 ## Set up final estimator and add to pipeline.
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172 estimator_json = params['final_estimator']['estimator_selector']
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173 if estimator_json['selected_module'] == 'none':
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174 if len(pipeline_steps) == 0:
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175 sys.exit("No pipeline steps specified!")
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176 ## else: turn the last pre-process component to final estimator
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177 else:
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178 estimator = get_estimator(estimator_json)
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179 pipeline_steps.append( estimator )
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180
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181 #if $output_type == 'Final_Estimator_Builder':
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182 with open('$outfile', 'wb') as out_handler:
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183 final_est = pipeline_steps[-1]
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184 print(final_est)
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185 pickle.dump(final_est, out_handler, pickle.HIGHEST_PROTOCOL)
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186 out_obj = final_est
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187 #else:
7
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188 if has_imblearn:
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189 pipeline = imb_make_pipeline(*pipeline_steps)
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190 else:
8
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191 pipeline = make_pipeline(*pipeline_steps)
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192 pprint.pprint(pipeline.named_steps)
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193
7
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194 with open('$outfile', 'wb') as out_handler:
0
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195 pickle.dump(pipeline, out_handler, pickle.HIGHEST_PROTOCOL)
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196 out_obj = pipeline
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197 #end if
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198
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199 #if $get_params
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200 results = get_search_params(out_obj)
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201 df = pd.DataFrame(results, columns=['', 'Parameter', 'Value'])
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202 df.to_csv('$outfile_params', sep='\t', index=False)
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203 #end if
0
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204 ]]>
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205 </configfile>
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206 </configfiles>
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207 <inputs>
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208 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step">
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209 <conditional name="component_selector">
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210 <param name="component_type" type="select" label="Choose the type of transformation:">
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211 <option value="None" selected="true">None</option>
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212 <option value="pre_processor">Sklearn Preprocessor</option>
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213 <option value="feature_selection">Feature Selection</option>
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214 <option value="decomposition">Matrix Decomposition</option>
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215 <option value="kernel_approximation">Kernel Approximation</option>
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216 <option value="FeatureAgglomeration">Agglomerate Features</option>
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217 <option value="skrebate">SK-rebate Feature Selection</option>
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218 <option value="imblearn">Imbalanced-learn Sampling</option>
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219 <option value="IRAPS">IRAPS -- feature selector and classifier</option>
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220 <option value="preprocessors">Bio-sequence Encoders</option>
0
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221 </param>
3
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222 <when value="None"/>
0
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223 <when value="pre_processor">
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224 <conditional name="pre_processors">
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225 <expand macro="sparse_preprocessors_ext" />
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226 <expand macro="sparse_preprocessor_options_ext" />
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227 </conditional>
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228 </when>
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229 <when value="feature_selection">
7
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230 <expand macro="feature_selection_pipeline"/>
0
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231 </when>
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232 <when value="decomposition">
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233 <expand macro="matrix_decomposition_all"/>
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234 </when>
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235 <when value="kernel_approximation">
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236 <expand macro="kernel_approximation_all"/>
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237 </when>
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238 <when value="FeatureAgglomeration">
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239 <expand macro="FeatureAgglomeration"/>
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240 </when>
3
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241 <when value="skrebate">
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diff changeset
242 <expand macro="skrebate"/>
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243 </when>
7
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diff changeset
244 <when value="imblearn">
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diff changeset
245 <expand macro="imbalanced_learn_sampling"/>
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246 </when>
8
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247 <when value="IRAPS">
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248 <expand macro="estimator_params_text"
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249 label="Type in parameter settings for IRAPSCore if different from default:"
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250 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes"/>
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251 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001"/>
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252 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1"/>
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253 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7"/>
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254 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1"/>
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255 </when>
10
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256 <when value="preprocessors">
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diff changeset
257 <expand macro="preprocessors_sequence_encoders"/>
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258 </when>
0
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259 </conditional>
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260 </repeat>
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261 <section name="final_estimator" title="Final Estimator" expanded="true">
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262 <conditional name="estimator_selector">
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263 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
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264 <expand macro="estimator_module_options">
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265 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
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266 <option value="custom_estimator">Load a custom estimator</option>
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267 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
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268 </expand>
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269 </param>
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270 <expand macro="estimator_suboptions">
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271 <when value="binarize_target">
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272 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
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273 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
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274 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
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275 </param>
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276 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline"/>
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277 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score"/>
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278 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None."/>
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279 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?"/>
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280 </when>
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281 <when value="custom_estimator">
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282 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/>
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283 </when>
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284 <when value="none"/>
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285 </expand>
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286 </conditional>
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287 </section>
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288 <param name="output_type" type="select" label="Output the final estimator instead?">
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289 <option value="Pipeline_Builder" selected="true">Pipeline</option>
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290 <option value="Final_Estimator_Builder">Final Estimator</option>
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291 </param>
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292 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?"
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293 help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool."/>
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294 </inputs>
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295 <outputs>
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296 <data format="zip" name="outfile" label="${output_type}"/>
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297 <data format="tabular" name="outfile_params" label="get_params for ${output_type}">
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298 <filter>get_params</filter>
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299 </data>
0
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300 </outputs>
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301 <tests>
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302 <test>
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303 <repeat name="pipeline_component">
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304 <conditional name="component_selector">
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305 <param name="component_type" value="pre_processor"/>
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306 <conditional name="pre_processors">
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307 <param name="selected_pre_processor" value="RobustScaler"/>
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308 </conditional>
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309 </conditional>
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310 </repeat>
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311 <repeat name="pipeline_component">
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312 <conditional name="component_selector">
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313 <param name="component_type" value="feature_selection"/>
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314 <conditional name="fs_algorithm_selector">
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315 <param name="selected_algorithm" value="SelectKBest"/>
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316 <param name="score_func" value="f_classif"/>
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317 </conditional>
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318 </conditional>
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319 </repeat>
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320 <param name="selected_module" value="svm"/>
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321 <param name="selected_estimator" value="SVR"/>
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322 <param name="text_params" value="kernel='linear'"/>
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323 <output name="outfile" file="pipeline01" compare="sim_size" delta="5"/>
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324 </test>
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325 <test>
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326 <conditional name="component_selector">
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327 <param name="component_type" value="pre_processor"/>
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328 <conditional name="pre_processors">
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329 <param name="selected_pre_processor" value="RobustScaler"/>
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330 </conditional>
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331 </conditional>
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332 <param name="selected_module" value="linear_model"/>
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333 <param name="selected_estimator" value="LassoCV"/>
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334 <output name="outfile" file="pipeline02" compare="sim_size" delta="5"/>
0
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335 </test>
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336 <test>
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337 <conditional name="component_selector">
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338 <param name="component_type" value="pre_processor"/>
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339 <conditional name="pre_processors">
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340 <param name="selected_pre_processor" value="RobustScaler"/>
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341 </conditional>
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342 </conditional>
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343 <param name="selected_module" value="xgboost"/>
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344 <param name="selected_estimator" value="XGBClassifier"/>
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345 <output name="outfile" file="pipeline03" compare="sim_size" delta="5"/>
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346 </test>
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347 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
348 <conditional name="component_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
349 <param name="component_type" value="feature_selection"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
350 <conditional name="fs_algorithm_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
351 <param name="selected_algorithm" value="SelectFromModel"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
352 <conditional name="model_inputter">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
353 <conditional name="estimator_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
354 <param name="selected_module" value="ensemble"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
355 <param name="selected_estimator" value="AdaBoostClassifier"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
356 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
357 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
358 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
359 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
360 <section name="final_estimator">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
361 <param name="selected_module" value="svm"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
362 <param name="selected_estimator" value="LinearSVC"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
363 </section>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
364 <output name="outfile" file="pipeline04" compare="sim_size" delta="5"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
365 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
366 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
367 <conditional name="component_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
368 <param name="component_type" value="None"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
369 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
370 <param name="selected_module" value="ensemble"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
371 <param name="selected_estimator" value="RandomForestRegressor"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
372 <param name="text_params" value="n_estimators=100, random_state=42"/>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
373 <output name="outfile" file="pipeline05" compare="sim_size" delta="5"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
374 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
375 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
376 <conditional name="component_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
377 <param name="component_type" value="decomposition"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
378 <conditional name="matrix_decomposition_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
379 <param name="select_algorithm" value="PCA"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
380 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
381 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
382 <param name="selected_module" value="ensemble"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
383 <param name="selected_estimator" value="AdaBoostRegressor"/>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
384 <output name="outfile" file="pipeline06" compare="sim_size" delta="5"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
385 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
386 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
387 <conditional name="component_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
388 <param name="component_type" value="kernel_approximation"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
389 <conditional name="kernel_approximation_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
390 <param name="select_algorithm" value="RBFSampler"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
391 <param name="text_params" value="n_components=10, gamma=2.0"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
392 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
393 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
394 <param name="selected_module" value="ensemble"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
395 <param name="selected_estimator" value="AdaBoostClassifier"/>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
396 <output name="outfile" file="pipeline07" compare="sim_size" delta="5"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
397 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
398 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
399 <conditional name="component_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
400 <param name="component_type" value="FeatureAgglomeration"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
401 <conditional name="FeatureAgglomeration_selector">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
402 <param name="select_algorithm" value="FeatureAgglomeration"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
403 <param name="text_params" value="n_clusters=3, affinity='euclidean'"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
404 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
405 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
406 <param name="selected_module" value="ensemble"/>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
407 <param name="selected_estimator" value="AdaBoostClassifier"/>
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
408 <output name="outfile" file="pipeline08" compare="sim_size" delta="20"/>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
409 </test>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
410 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
411 <conditional name="component_selector">
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
412 <param name="component_type" value="skrebate"/>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
413 <conditional name="skrebate_selector">
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
414 <param name="select_algorithm" value="ReliefF"/>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
415 <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
416 </conditional>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
417 </conditional>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
418 <param name="selected_module" value="ensemble"/>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
419 <param name="selected_estimator" value="RandomForestRegressor"/>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
420 <output name="outfile" file="pipeline09" compare="sim_size" delta="5"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
421 </test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
422 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
423 <conditional name="component_selector">
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
424 <param name="component_type" value="None"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
425 </conditional>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
426 <param name="selected_module" value="ensemble"/>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
427 <param name="selected_estimator" value="AdaBoostRegressor"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
428 <output name="outfile" file="pipeline10" compare="sim_size" delta="5"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
429 </test>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
430 <test>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
431 <conditional name="component_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
432 <param name="component_type" value="imblearn"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
433 <conditional name="imblearn_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
434 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
435 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
436 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
437 <param name="selected_module" value="ensemble"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
438 <param name="selected_estimator" value="RandomForestClassifier"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
439 <output name="outfile" file="pipeline11" compare="sim_size" delta="5"/>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
440 </test>
6
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
441 <test expect_failure="true">
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
442 <conditional name="component_selector">
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
443 <param name="component_type" value="None"/>
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
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444 </conditional>
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
445 <param name="selected_module" value="ensemble"/>
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
446 <param name="selected_estimator" value="RandomForestRegressor"/>
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
447 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')"/>
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
448 </test>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
449 <test>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
450 <conditional name="component_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
451 <param name="component_type" value="feature_selection"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
452 <conditional name="fs_algorithm_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
453 <param name="selected_algorithm" value="RFE"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
454 <conditional name="estimator_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
455 <param name="selected_module" value="xgboost"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
456 <param name="selected_estimator" value="XGBRegressor"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
457 <param name="text_params" value="random_state=0"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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458 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
459 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
460 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
461 <section name="final_estimator">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
462 <conditional name="estimator_selector">
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
463 <param name="selected_module" value="none"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
464 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
465 </section>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
466 <output name="outfile" file="pipeline12" compare="sim_size" delta="5"/>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
467 </test>
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
468 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
469 <conditional name="component_selector">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
470 <param name="component_type" value="None"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
471 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
472 <param name="selected_module" value="ensemble"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
473 <param name="selected_estimator" value="RandomForestClassifier"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
474 <param name="output_type" value="Final_Estimator_Builder"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
475 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="5"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
476 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
477 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
478 <conditional name="component_selector">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
479 <param name="component_type" value="IRAPS"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
480 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
481 <section name="final_estimator">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
482 <conditional name="estimator_selector">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
483 <param name="selected_module" value="none"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
484 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
485 </section>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
486 <param name="output_type" value="Final_Estimator_Builder"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
487 <output name="outfile" file="pipeline14" compare="sim_size" delta="5"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
488 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
489 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
490 <conditional name="component_selector">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
491 <param name="component_type" value="None"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
492 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
493 <section name="final_estimator">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
494 <conditional name="estimator_selector">
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
495 <param name="selected_module" value="binarize_target"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
496 <param name="clf_or_regr" value="BinarizeTargetClassifier"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
497 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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498 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
499 </section>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
500 <param name="output_type" value="Final_Estimator_Builder"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
501 <output name="outfile" file="pipeline15" compare="sim_size" delta="5"/>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
502 </test>
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
503 <test>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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504 <conditional name="component_selector">
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
505 <param name="component_type" value="preprocessors"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
506 <conditional name="encoder_selection">
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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507 <param name="encoder_type" value="GenomeOneHotEncoder"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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508 <param name="seq_length" value="1000"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
509 <param name="padding" value="True"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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510 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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511 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
512 <section name="final_estimator">
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
513 <conditional name="estimator_selector">
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
514 <param name="selected_module" value="custom_estimator"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
515 <param name="c_estimator" value="keras_model02" ftype="zip"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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516 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
517 </section>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
518 <output name="outfile" file="pipeline16" compare="sim_size" delta="5"/>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
519 </test>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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520 </tests>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
521 <help>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
522 <![CDATA[
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
523 **What it does**
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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524 Constructs a pipeline that contains a list of transfroms and a final estimator. Pipeline assembles several steps
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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525 that can be cross-validated together while setting different parameters.
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526 please refer to `Scikit-learn pipeline Pipeline`_.
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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527
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528 **Pre-processing components** allow None, one or a combination of up to 5 transformations from `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_ and/or `skrebate`_.
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529
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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530 **Estimator** selector supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_ and `neighbors`_.
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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531
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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532
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533 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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534 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
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535 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
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536 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
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537 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
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538 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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539 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
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540 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
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541
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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542 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
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543 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
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544 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
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545 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
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546 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
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547 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
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548
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549 ]]>
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550 </help>
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551 <expand macro="sklearn_citation">
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552 <expand macro="skrebate_citation"/>
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553 <expand macro="xgboost_citation"/>
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554 <expand macro="imblearn_citation"/>
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555 </expand>
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556 </tool>