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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author bgruening
date Mon, 02 Oct 2023 07:50:10 +0000
parents 15815a470e6b
children
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="@PROFILE@">
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2 <description>an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers</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 pprint
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22 import skrebate
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23 import sys
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24 import warnings
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25 from sklearn import (
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26 cluster, compose, decomposition, ensemble, feature_extraction,
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27 feature_selection, gaussian_process, kernel_approximation, metrics,
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28 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
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29 svm, linear_model, tree, discriminant_analysis)
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30 from sklearn.pipeline import make_pipeline
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31 from imblearn.pipeline import make_pipeline as imb_make_pipeline
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32 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
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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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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':
0
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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 elif estimator_json['selected_module'] == 'sklearn.compose':
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178 #if $final_estimator.estimator_selector.selected_module == 'sklearn.compose':
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179 regressor_path = '$final_estimator.estimator_selector.regressor'
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180 transformer_path = '$final_estimator.estimator_selector.transformer'
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181 #end if
24
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182 regressor = load_model_from_h5(regressor_path)
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183 transformer = load_model_from_h5(transformer_path)
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184 estimator = compose.TransformedTargetRegressor(regressor=regressor, transformer=transformer)
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185 pipeline_steps.append( estimator )
7
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186 else:
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187 estimator = get_estimator(estimator_json)
8
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188 pipeline_steps.append( estimator )
0
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189
15
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190 if len(pipeline_steps) == 1:
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191 out_obj = pipeline_steps[-1]
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192 print(out_obj)
7
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193 else:
15
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194 if has_imblearn:
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195 out_obj = imb_make_pipeline(*pipeline_steps)
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196 else:
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197 out_obj = make_pipeline(*pipeline_steps)
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198 pprint.pprint(out_obj.named_steps)
0
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199
24
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200 dump_model_to_h5(out_obj, '$outfile', verbose=0)
10
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201
0
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202 ]]>
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203 </configfile>
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204 </configfiles>
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205 <inputs>
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206 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step">
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207 <conditional name="component_selector">
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208 <param name="component_type" type="select" label="Choose the type of transformation:">
3
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209 <option value="None" selected="true">None</option>
0
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210 <option value="pre_processor">Sklearn Preprocessor</option>
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211 <option value="feature_selection">Feature Selection</option>
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212 <option value="decomposition">Matrix Decomposition</option>
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213 <option value="kernel_approximation">Kernel Approximation</option>
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214 <option value="FeatureAgglomeration">Agglomerate Features</option>
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215 <option value="skrebate">SK-rebate Feature Selection</option>
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216 <option value="imblearn">Imbalanced-learn Sampling</option>
8
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217 <option value="IRAPS">IRAPS -- feature selector and classifier</option>
10
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218 <option value="preprocessors">Bio-sequence Encoders</option>
0
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219 </param>
18
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220 <when value="None" />
0
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221 <when value="pre_processor">
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222 <conditional name="pre_processors">
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223 <expand macro="sparse_preprocessors_ext" />
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224 <expand macro="sparse_preprocessor_options_ext" />
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225 </conditional>
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226 </when>
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227 <when value="feature_selection">
18
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228 <expand macro="feature_selection_pipeline" />
0
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229 </when>
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230 <when value="decomposition">
18
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231 <expand macro="matrix_decomposition_all" />
0
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232 </when>
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233 <when value="kernel_approximation">
18
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234 <expand macro="kernel_approximation_all" />
0
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235 </when>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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236 <when value="FeatureAgglomeration">
18
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237 <expand macro="FeatureAgglomeration" />
0
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238 </when>
3
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diff changeset
239 <when value="skrebate">
18
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240 <expand macro="skrebate" />
3
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241 </when>
7
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242 <when value="imblearn">
18
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243 <expand macro="imbalanced_learn_sampling" />
7
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244 </when>
8
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245 <when value="IRAPS">
24
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diff changeset
246 <expand macro="estimator_params_text"
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247 label="Type in parameter settings for IRAPSCore if different from default:"
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248 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes" />
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249 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" />
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250 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" />
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251 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" />
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252 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" />
8
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253 </when>
10
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254 <when value="preprocessors">
18
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255 <expand macro="preprocessors_sequence_encoders" />
10
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256 </when>
0
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257 </conditional>
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258 </repeat>
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259 <section name="final_estimator" title="Final Estimator" expanded="true">
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260 <conditional name="estimator_selector">
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261 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
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262 <expand macro="estimator_module_options">
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263 <option value="sklearn.compose">sklearn.compose</option>
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264 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
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265 <option value="custom_estimator">Load a custom estimator</option>
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266 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
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267 </expand>
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268 </param>
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269 <expand macro="estimator_suboptions">
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270 <when value="sklearn.compose">
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271 <param name="selected_estimator" type="select" label="Choose estimator class:">
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272 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
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273 </param>
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274 <param name="regressor" type="data" format="h5mlm" label="Choose the dataset containing the wrapped regressor" />
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275 <param name="transformer" type="data" format="h5mlm" label="Choose the dataset containing transformer" />
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276 </when>
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277 <when value="binarize_target">
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278 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
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279 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
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280 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
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281 </param>
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282 <param name="wrapped_estimator" type="data" format="h5mlm" label="Choose the dataset containing the wrapped estimator or pipeline" />
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283 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" />
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284 <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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285 <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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286 </when>
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287 <when value="custom_estimator">
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288 <param name="c_estimator" type="data" format="h5mlm" label="Choose the dataset containing the custom estimator or pipeline" />
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289 </when>
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290 <when value="none" />
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291 </expand>
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292 </conditional>
0
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293 </section>
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294 <!--param name="output_type" type="select" label="Output the final estimator instead?">
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295 <option value="Pipeline_Builder" selected="true">Pipeline</option>
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296 <option value="Final_Estimator_Builder">Final Estimator</option>
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297 </param>-->
0
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298 </inputs>
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299 <outputs>
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300 <data format="h5mlm" name="outfile" label="New Pipleline/Estimator" />
0
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301 </outputs>
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302 <tests>
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303 <test>
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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="QuantileTransformer" />
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308 <section name="options">
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309 <param name="random_state" value="10" />
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310 </section>
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311 </conditional>
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312 </conditional>
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313 <section name="final_estimator">
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314 <conditional name="estimator_selector">
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315 <param name="selected_module" value="none" />
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316 </conditional>
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317 </section>
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318 <output name="outfile" file="pipeline17" compare="sim_size" delta="5" />
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319 </test>
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320 <test>
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321 <conditional name="component_selector">
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322 <param name="component_type" value="pre_processor" />
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323 <conditional name="pre_processors">
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324 <param name="selected_pre_processor" value="PowerTransformer" />
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325 </conditional>
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326 </conditional>
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327 <section name="final_estimator">
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328 <conditional name="estimator_selector">
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329 <param name="selected_module" value="sklearn.compose" />
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330 <param name="regressor" value="RandomForestRegressor01.h5mlm" ftype="h5mlm" />
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331 <param name="transformer" value="pipeline17" ftype="h5mlm" />
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332 </conditional>
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333 </section>
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334 <output name="outfile" file="pipeline18" compare="sim_size" delta="5" />
15
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335 </test>
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336 <test>
0
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337 <repeat name="pipeline_component">
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338 <conditional name="component_selector">
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339 <param name="component_type" value="pre_processor" />
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340 <conditional name="pre_processors">
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341 <param name="selected_pre_processor" value="RobustScaler" />
0
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342 </conditional>
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343 </conditional>
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diff changeset
344 </repeat>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
345 <repeat name="pipeline_component">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
346 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
347 <param name="component_type" value="feature_selection" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
348 <conditional name="fs_algorithm_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
349 <param name="selected_algorithm" value="SelectKBest" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
350 <param name="score_func" value="f_classif" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
351 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
352 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
353 </repeat>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
354 <param name="selected_module" value="svm" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
355 <param name="selected_estimator" value="SVR" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
356 <param name="text_params" value="kernel='linear'" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
357 <output name="outfile" file="pipeline01" 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
358 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
359 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
360 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
361 <param name="component_type" value="pre_processor" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
362 <conditional name="pre_processors">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
363 <param name="selected_pre_processor" value="RobustScaler" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
364 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
365 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
366 <param name="selected_module" value="linear_model" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
367 <param name="selected_estimator" value="LassoCV" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
368 <output name="outfile" file="pipeline02" 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
369 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
370 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
371 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
372 <param name="component_type" value="pre_processor" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
373 <conditional name="pre_processors">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
374 <param name="selected_pre_processor" value="RobustScaler" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
375 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
376 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
377 <param name="selected_module" value="xgboost" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
378 <param name="selected_estimator" value="XGBClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
379 <output name="outfile" file="pipeline03" 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
380 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
381 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
382 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
383 <param name="component_type" value="feature_selection" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
384 <conditional name="fs_algorithm_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
385 <param name="selected_algorithm" value="SelectFromModel" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
386 <conditional name="model_inputter">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
387 <conditional name="estimator_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
388 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
389 <param name="selected_estimator" value="AdaBoostClassifier" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
390 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
391 </conditional>
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 <section name="final_estimator">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
395 <param name="selected_module" value="svm" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
396 <param name="selected_estimator" value="LinearSVC" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
397 </section>
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
398 <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
399 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
400 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
401 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
402 <param name="component_type" value="None" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
403 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
404 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
405 <param name="selected_estimator" value="RandomForestRegressor" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
406 <param name="text_params" value="n_estimators=100, random_state=42" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
407 <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
408 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
409 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
410 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
411 <param name="component_type" value="decomposition" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
412 <conditional name="matrix_decomposition_selector">
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
413 <param name="select_algorithm" value="PCA" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
414 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
415 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
416 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
417 <param name="selected_estimator" value="AdaBoostRegressor" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
418 <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
419 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
420 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
421 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
422 <param name="component_type" value="kernel_approximation" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
423 <conditional name="kernel_approximation_selector">
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
424 <param name="select_algorithm" value="RBFSampler" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
425 <param name="text_params" value="n_components=10, gamma=2.0" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
426 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
427 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
428 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
429 <param name="selected_estimator" value="AdaBoostClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
430 <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
431 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
432 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
433 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
434 <param name="component_type" value="FeatureAgglomeration" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
435 <conditional name="FeatureAgglomeration_selector">
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
436 <param name="select_algorithm" value="FeatureAgglomeration" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
437 <param name="text_params" value="n_clusters=3, affinity='euclidean'" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
438 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
439 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
440 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
441 <param name="selected_estimator" value="AdaBoostClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
442 <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
443 </test>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
444 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
445 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
446 <param name="component_type" value="skrebate" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
447 <conditional name="skrebate_selector">
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
448 <param name="select_algorithm" value="ReliefF" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
449 <param name="text_params" value="n_features_to_select=3, n_neighbors=100" />
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
450 </conditional>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
451 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
452 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
453 <param name="selected_estimator" value="RandomForestRegressor" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
454 <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
455 </test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
456 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
457 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
458 <param name="component_type" value="imblearn" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
459 <conditional name="imblearn_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
460 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
461 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
462 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
463 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
464 <param name="selected_estimator" value="RandomForestClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
465 <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
466 </test>
6
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
467 <test expect_failure="true">
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
468 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
469 <param name="component_type" value="None" />
6
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
470 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
471 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
472 <param name="selected_estimator" value="RandomForestRegressor" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
473 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')" />
6
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
474 </test>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
475 <test>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
476 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
477 <param name="component_type" value="feature_selection" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
478 <conditional name="fs_algorithm_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
479 <param name="selected_algorithm" value="RFE" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
480 <conditional name="estimator_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
481 <param name="selected_module" value="xgboost" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
482 <param name="selected_estimator" value="XGBRegressor" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
483 <param name="text_params" value="random_state=0" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
484 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
485 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
486 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
487 <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
488 <conditional name="estimator_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
489 <param name="selected_module" value="none" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
490 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
491 </section>
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
492 <output name="outfile" file="pipeline12" compare="sim_size" delta="5" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
493 </test>
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
494 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
495 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
496 <param name="component_type" value="None" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
497 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
498 <param name="selected_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
499 <param name="selected_estimator" value="RandomForestClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
500 <output name="outfile" file="RandomForestClassifier.h5mlm" compare="sim_size" delta="5" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
501 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
502 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
503 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
504 <param name="component_type" value="IRAPS" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
505 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
506 <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
507 <conditional name="estimator_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
508 <param name="selected_module" value="none" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
509 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
510 </section>
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 18
diff changeset
511 <output name="outfile" file="pipeline14" compare="sim_size" delta="5" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
512 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
513 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
514 <conditional name="component_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
515 <param name="component_type" value="None" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
516 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
517 <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
518 <conditional name="estimator_selector">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
519 <param name="selected_module" value="binarize_target" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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520 <param name="clf_or_regr" value="BinarizeTargetClassifier" />
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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521 <param name="wrapped_estimator" value="RandomForestClassifier.h5mlm" ftype="h5mlm" />
8
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522 </conditional>
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523 </section>
24
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524 <output name="outfile" file="pipeline15" compare="sim_size" delta="5" />
8
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diff changeset
525 </test>
10
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diff changeset
526 <test>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
527 <conditional name="component_selector">
18
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528 <param name="component_type" value="preprocessors" />
10
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529 <conditional name="encoder_selection">
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530 <param name="encoder_type" value="GenomeOneHotEncoder" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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531 <param name="seq_length" value="1000" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
532 <param name="padding" value="True" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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533 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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534 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
535 <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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536 <conditional name="estimator_selector">
18
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537 <param name="selected_module" value="custom_estimator" />
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538 <param name="c_estimator" value="keras_model02" ftype="h5mlm" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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539 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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540 </section>
24
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541 <output name="outfile" file="pipeline16" compare="sim_size" delta="5" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
542 </test>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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543 </tests>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
544 <help>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
545 <![CDATA[
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
546 **What it does**
15
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diff changeset
547 This tool not only builds sklearn pipeline object, but also builds single main estimator or single preprocessing component. The output object type is based on the length of pipeline steps. When there is only one step (choose `None` for others), either a main estimator or preprocessor, the component is output directly instead of wrapping in a pipeline object.
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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548
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
549 A typical pipeline chains one or more preprocessing steps plus a final main estimator, for example, [VarianceThreshold, StandardScaler, SGDClassifier] which is composed of a feature selctor, a preprocessing scaler and a main estimator together.
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
550 For more information, please refer to `Scikit-learn pipeline Pipeline`_.
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
551
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
552 **Pre-processing components** come from `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_, `skrebate`_ and more.
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
553
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
554 **Final Estimator** supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and so on.
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
555
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
556 **Custom estimators**
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
557
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
558 - `GenomeOneHotEncoder`_
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
559
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
560 - `ProteinOnehotEncoder`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
561
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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parents: 10
diff changeset
562 - `IRAPSClassifier`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
563
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
564 - `BinarizeTargetClassifier`_
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
565
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
566 - `BinarizeTargetRegressor`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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parents: 10
diff changeset
567
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
568 **Output**
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
569
24
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parents: 18
diff changeset
570 - Pipeline/estimator object
15
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bgruening
parents: 10
diff changeset
571
24
15815a470e6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
572 - Hyperparameter of the object (optional)
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
573
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
574
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
575 .. _`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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576 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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577 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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578 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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579 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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580 .. _`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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diff changeset
581 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
582 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
583
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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584 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
585 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
586 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
587 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
588 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
589 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
590
15
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diff changeset
591 .. _`GenomeOneHotEncoder`: https://goeckslab.github.io/Galaxy-ML/APIs/preprocessors/#genomeonehotencoder
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
592 .. _`ProteinOnehotEncoder`: https://goeckslab.github.io/Galaxy-ML/APIs/preprocessors/#proteinonehotencoder
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
593 .. _`IRAPSClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/iraps-classifier/#irapsclassifier
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
594 .. _`BinarizeTargetClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetclassifier
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
595 .. _`BinarizeTargetRegressor`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetregressor
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
596
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
597 ]]>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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598 </help>
4
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diff changeset
599 <expand macro="sklearn_citation">
18
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diff changeset
600 <expand macro="skrebate_citation" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
601 <expand macro="xgboost_citation" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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602 <expand macro="imblearn_citation" />
4
9e189ce7d859 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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603 </expand>
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f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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604 </tool>