Mercurial > repos > bgruening > sklearn_build_pipeline

annotate pipeline.xml @ 19:866dec0ace48 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
author bgruening
date Tue, 20 Apr 2021 16:57:34 +0000
parents 449bd57f70f4
children 15815a470e6b
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="20.05">
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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 pickle
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22 import pprint
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23 import skrebate
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24 import sys
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25 import warnings
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26 from sklearn import (
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27 cluster, compose, decomposition, ensemble, feature_extraction,
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28 feature_selection, gaussian_process, kernel_approximation, metrics,
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29 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
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30 svm, linear_model, tree, discriminant_analysis)
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31 from sklearn.pipeline import make_pipeline
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32 from imblearn.pipeline import make_pipeline as imb_make_pipeline
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33 from galaxy_ml.utils import (SafeEval, feature_selector, get_estimator,
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34 try_get_attr, get_search_params, load_model)
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36 ## TODO remove following imports after scikit-learn v0.22
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37 from sklearn.experimental import enable_hist_gradient_boosting
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40 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
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42 warnings.filterwarnings('ignore')
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44 safe_eval = SafeEval()
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46 input_json_path = sys.argv[1]
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47 with open(input_json_path, 'r') as param_handler:
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48 params = json.load(param_handler)
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49
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50 #if $final_estimator.estimator_selector.selected_module == 'custom_estimator':
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51 params['final_estimator']['estimator_selector']['c_estimator'] =\
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52 '$final_estimator.estimator_selector.c_estimator'
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53 #end if
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54
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55 #if $final_estimator.estimator_selector.selected_module == 'binarize_target':
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56 params['final_estimator']['estimator_selector']['wrapped_estimator'] =\
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57 '$final_estimator.estimator_selector.wrapped_estimator'
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58 #end if
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59
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60 pipeline_steps = []
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61
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62 def get_component(input_json, check_none=False):
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63 is_imblearn = False
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64 if input_json['component_type'] == 'None':
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65 if not check_none:
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66 return None, False
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67 else:
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68 sys.exit("The pre-processing component type can't be None "
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69 "when the number of components is greater than 1.")
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70 if input_json['component_type'] == 'pre_processor':
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71 preprocessor = input_json['pre_processors']['selected_pre_processor']
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72 pre_processor_options = input_json['pre_processors']['options']
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73 if 'feature_range' in pre_processor_options:
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74 feature_range = safe_eval(pre_processor_options['feature_range'].strip())
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75 if not feature_range:
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76 feature_range = (0, 1)
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77 pre_processor_options['feature_range'] = feature_range
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78 my_class = getattr(preprocessing, preprocessor)
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79 obj = my_class(**pre_processor_options)
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80 elif input_json['component_type'] == 'feature_selection':
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81 obj = feature_selector(input_json['fs_algorithm_selector'])
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82 elif input_json['component_type'] == 'decomposition':
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83 algorithm = input_json['matrix_decomposition_selector']['select_algorithm']
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84 obj = getattr(decomposition, algorithm)()
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85 options = input_json['matrix_decomposition_selector']['text_params'].strip()
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86 if options != '':
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diff changeset
87 options = safe_eval( 'dict(' + options + ')' )
0
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88 obj.set_params(**options)
3
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89 elif input_json['component_type'] == 'kernel_approximation':
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90 algorithm = input_json['kernel_approximation_selector']['select_algorithm']
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91 obj = getattr(kernel_approximation, algorithm)()
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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92 options = input_json['kernel_approximation_selector']['text_params'].strip()
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93 if options != '':
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94 options = safe_eval( 'dict(' + options + ')' )
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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95 obj.set_params(**options)
3
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96 elif input_json['component_type'] == 'FeatureAgglomeration':
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97 algorithm = input_json['FeatureAgglomeration_selector']['select_algorithm']
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98 obj = getattr(cluster, algorithm)()
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99 options = input_json['FeatureAgglomeration_selector']['text_params'].strip()
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100 if options != '':
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101 options = safe_eval( 'dict(' + options + ')' )
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102 obj.set_params(**options)
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103 elif input_json['component_type'] == 'skrebate':
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104 algorithm = input_json['skrebate_selector']['select_algorithm']
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105 if algorithm == 'TuRF':
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106 obj = getattr(skrebate, algorithm)(core_algorithm='ReliefF')
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107 else:
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108 obj = getattr(skrebate, algorithm)()
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109 options = input_json['skrebate_selector']['text_params'].strip()
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110 if options != '':
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111 options = safe_eval( 'dict(' + options + ')' )
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112 obj.set_params(**options)
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113 elif input_json['component_type'] == 'imblearn':
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114 is_imblearn = True
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115 algorithm = input_json['imblearn_selector']['select_algorithm']
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116 if algorithm == 'over_sampling.SMOTENC':
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117 obj = over_sampling.SMOTENC(categorical_features=[])
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118 elif algorithm == 'Z_RandomOverSampler':
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119 Z_RandomOverSampler = try_get_attr('galaxy_ml.preprocessors',
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120 'Z_RandomOverSampler')
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diff changeset
121 obj = Z_RandomOverSampler()
7
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122 else:
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diff changeset
123 globals = algorithm.split('.')
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124 mod, klass = globals[0], globals[1]
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125 obj = getattr(getattr(imblearn, mod), klass)()
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126 options = input_json['imblearn_selector']['text_params'].strip()
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127 if options != '':
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128 options = safe_eval( 'dict(' + options + ')' )
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129 obj.set_params(**options)
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130 elif input_json['component_type'] == 'IRAPS':
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131 iraps_core = try_get_attr('galaxy_ml.iraps_classifier','IRAPSCore')()
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132 core_params = input_json['text_params'].strip()
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133 if core_params != '':
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diff changeset
134 try:
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135 params = safe_eval('dict(' + core_params + ')')
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136 except ValueError:
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137 sys.exit("Unsupported parameter input: `%s`" % core_params)
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diff changeset
138 iraps_core.set_params(**params)
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139 options = {}
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140 if input_json['p_thres'] is not None:
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141 options['p_thres'] = input_json['p_thres']
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142 if input_json['fc_thres'] is not None:
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143 options['fc_thres'] = input_json['fc_thres']
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144 if input_json['occurrence'] is not None:
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145 options['occurrence'] = input_json['occurrence']
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146 if input_json['discretize'] is not None:
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147 options['discretize'] = input_json['discretize']
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diff changeset
148 IRAPSClassifier = try_get_attr('galaxy_ml.iraps_classifier','IRAPSClassifier')
8
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149 obj = IRAPSClassifier(iraps_core, **options)
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150 elif input_json['component_type'] == 'preprocessors':
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151 encoder_selection = input_json['encoder_selection']
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152 encoder_type = encoder_selection.pop('encoder_type')
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153 klass = try_get_attr('galaxy_ml.preprocessors', encoder_type)
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154 obj = klass(**encoder_selection)
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155
3
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diff changeset
156 if 'n_jobs' in obj.get_params():
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diff changeset
157 obj.set_params( n_jobs=N_JOBS )
7
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diff changeset
158 return obj, is_imblearn
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diff changeset
159
7
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diff changeset
160 has_imblearn = False
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161 if len(params['pipeline_component']) == 1:
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diff changeset
162 step_obj, is_imblearn = get_component( params['pipeline_component'][0]['component_selector'])
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163 if step_obj:
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diff changeset
164 pipeline_steps.append( step_obj )
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165 if is_imblearn:
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166 has_imblearn = True
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167 else:
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168 for i, c in enumerate(params['pipeline_component']):
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169 step_obj, is_imblearn = get_component( c['component_selector'], check_none=True )
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170 pipeline_steps.append( step_obj )
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171 if is_imblearn:
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172 has_imblearn = True
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173
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174 ## Set up final estimator and add to pipeline.
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175 estimator_json = params['final_estimator']['estimator_selector']
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176 if estimator_json['selected_module'] == 'none':
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177 if len(pipeline_steps) == 0:
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178 sys.exit("No pipeline steps specified!")
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179 ## else: turn the last pre-process component to final estimator
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180 elif estimator_json['selected_module'] == 'sklearn.compose':
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181 #if $final_estimator.estimator_selector.selected_module == 'sklearn.compose':
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182 regressor_path = '$final_estimator.estimator_selector.regressor'
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183 transformer_path = '$final_estimator.estimator_selector.transformer'
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184 #end if
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185 with open(regressor_path, 'rb') as f:
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186 regressor = load_model(f)
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187 with open(transformer_path, 'rb') as f:
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188 transformer = load_model(f)
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189 estimator = compose.TransformedTargetRegressor(regressor=regressor, transformer=transformer)
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190 pipeline_steps.append( estimator )
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191 else:
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192 estimator = get_estimator(estimator_json)
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193 pipeline_steps.append( estimator )
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194
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195 if len(pipeline_steps) == 1:
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196 out_obj = pipeline_steps[-1]
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197 print(out_obj)
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198 else:
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199 if has_imblearn:
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200 out_obj = imb_make_pipeline(*pipeline_steps)
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201 else:
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202 out_obj = make_pipeline(*pipeline_steps)
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203 pprint.pprint(out_obj.named_steps)
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204
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205 with open('$outfile', 'wb') as out_handler:
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206 pickle.dump(out_obj, out_handler, pickle.HIGHEST_PROTOCOL)
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207
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208 #if $get_params
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209 results = get_search_params(out_obj)
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210 df = pd.DataFrame(results, columns=['', 'Parameter', 'Value'])
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211 df.to_csv('$outfile_params', sep='\t', index=False)
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212 #end if
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213 ]]>
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214 </configfile>
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215 </configfiles>
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216 <inputs>
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217 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step">
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218 <conditional name="component_selector">
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219 <param name="component_type" type="select" label="Choose the type of transformation:">
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220 <option value="None" selected="true">None</option>
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221 <option value="pre_processor">Sklearn Preprocessor</option>
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222 <option value="feature_selection">Feature Selection</option>
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223 <option value="decomposition">Matrix Decomposition</option>
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224 <option value="kernel_approximation">Kernel Approximation</option>
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225 <option value="FeatureAgglomeration">Agglomerate Features</option>
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226 <option value="skrebate">SK-rebate Feature Selection</option>
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227 <option value="imblearn">Imbalanced-learn Sampling</option>
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228 <option value="IRAPS">IRAPS -- feature selector and classifier</option>
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229 <option value="preprocessors">Bio-sequence Encoders</option>
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230 </param>
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231 <when value="None" />
0
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232 <when value="pre_processor">
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233 <conditional name="pre_processors">
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234 <expand macro="sparse_preprocessors_ext" />
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235 <expand macro="sparse_preprocessor_options_ext" />
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236 </conditional>
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237 </when>
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238 <when value="feature_selection">
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239 <expand macro="feature_selection_pipeline" />
0
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240 </when>
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241 <when value="decomposition">
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242 <expand macro="matrix_decomposition_all" />
0
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243 </when>
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244 <when value="kernel_approximation">
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245 <expand macro="kernel_approximation_all" />
0
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246 </when>
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247 <when value="FeatureAgglomeration">
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248 <expand macro="FeatureAgglomeration" />
0
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249 </when>
3
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250 <when value="skrebate">
18
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251 <expand macro="skrebate" />
3
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252 </when>
7
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253 <when value="imblearn">
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254 <expand macro="imbalanced_learn_sampling" />
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255 </when>
8
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256 <when value="IRAPS">
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257 <expand macro="estimator_params_text" label="Type in parameter settings for IRAPSCore if different from default:" help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes" />
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258 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" />
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259 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" />
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260 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" />
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261 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" />
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262 </when>
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263 <when value="preprocessors">
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264 <expand macro="preprocessors_sequence_encoders" />
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265 </when>
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266 </conditional>
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267 </repeat>
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268 <section name="final_estimator" title="Final Estimator" expanded="true">
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269 <conditional name="estimator_selector">
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270 <param name="selected_module" type="select" label="Choose the module that contains target estimator:">
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271 <expand macro="estimator_module_options">
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272 <option value="sklearn.compose">sklearn.compose</option>
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273 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
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274 <option value="custom_estimator">Load a custom estimator</option>
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275 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
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276 </expand>
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277 </param>
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278 <expand macro="estimator_suboptions">
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279 <when value="sklearn.compose">
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280 <param name="selected_estimator" type="select" label="Choose estimator class:">
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281 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
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282 </param>
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283 <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor" />
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284 <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer" />
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285 </when>
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286 <when value="binarize_target">
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287 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
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288 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
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289 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
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290 </param>
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291 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline" />
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292 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" />
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293 <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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294 <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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295 </when>
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296 <when value="custom_estimator">
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297 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline" />
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298 </when>
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299 <when value="none" />
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300 </expand>
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301 </conditional>
0
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302 </section>
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303 <!--param name="output_type" type="select" label="Output the final estimator instead?">
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304 <option value="Pipeline_Builder" selected="true">Pipeline</option>
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305 <option value="Final_Estimator_Builder">Final Estimator</option>
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306 </param>-->
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307 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?" help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool." />
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308 </inputs>
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309 <outputs>
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310 <data format="zip" name="outfile" label="New Pipleline/Estimator" />
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311 <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator">
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312 <filter>get_params</filter>
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313 </data>
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314 </outputs>
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315 <tests>
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316 <test>
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317 <conditional name="component_selector">
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318 <param name="component_type" value="pre_processor" />
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319 <conditional name="pre_processors">
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320 <param name="selected_pre_processor" value="QuantileTransformer" />
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321 <section name="options">
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322 <param name="random_state" value="10" />
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323 </section>
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324 </conditional>
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325 </conditional>
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326 <section name="final_estimator">
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327 <conditional name="estimator_selector">
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328 <param name="selected_module" value="none" />
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329 </conditional>
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330 </section>
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331 <output name="outfile" file="pipeline17" compare="sim_size" delta="30" />
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332 </test>
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333 <test>
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334 <conditional name="component_selector">
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335 <param name="component_type" value="pre_processor" />
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336 <conditional name="pre_processors">
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337 <param name="selected_pre_processor" value="PowerTransformer" />
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338 </conditional>
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339 </conditional>
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340 <section name="final_estimator">
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341 <conditional name="estimator_selector">
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342 <param name="selected_module" value="sklearn.compose" />
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343 <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
344 <param name="transformer" value="pipeline17" ftype="zip" />
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
345 </conditional>
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
346 </section>
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="get_params" value="true" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
348 <output name="outfile_params" file="pipeline_params18" ftype="tabular" />
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
349 </test>
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
350 <test>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
351 <repeat name="pipeline_component">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
352 <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
353 <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
354 <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
355 <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
356 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
357 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
358 </repeat>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
359 <repeat name="pipeline_component">
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="feature_selection" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
362 <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
363 <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
364 <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
365 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
366 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
367 </repeat>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
368 <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
369 <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
370 <param name="text_params" value="kernel='linear'" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
371 <output name="outfile" file="pipeline01" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
372 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
373 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
374 <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
375 <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
376 <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
377 <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
378 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
379 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
380 <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
381 <param name="selected_estimator" value="LassoCV" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
382 <output name="outfile" file="pipeline02" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
383 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
384 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
385 <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
386 <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
387 <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
388 <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
389 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
390 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
391 <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
392 <param name="selected_estimator" value="XGBClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
393 <output name="outfile" file="pipeline03" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
394 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
395 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
396 <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
397 <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
398 <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
399 <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
400 <conditional name="model_inputter">
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
401 <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
402 <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
403 <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
404 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
405 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
406 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
407 </conditional>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
408 <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
409 <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
410 <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
411 </section>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
412 <output name="outfile" file="pipeline04" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
413 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
414 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
415 <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
416 <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
417 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
418 <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
419 <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
420 <param name="text_params" value="n_estimators=100, random_state=42" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
421 <param name="get_params" value="true" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
422 <output name="outfile" file="pipeline05" compare="sim_size" delta="30" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
423 <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
424 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
425 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
426 <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
427 <param name="component_type" value="decomposition" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
428 <conditional name="matrix_decomposition_selector">
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
429 <param name="select_algorithm" value="PCA" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
430 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
431 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
432 <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
433 <param name="selected_estimator" value="AdaBoostRegressor" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
434 <output name="outfile" file="pipeline06" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
435 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
436 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
437 <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
438 <param name="component_type" value="kernel_approximation" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
439 <conditional name="kernel_approximation_selector">
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
440 <param name="select_algorithm" value="RBFSampler" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
441 <param name="text_params" value="n_components=10, gamma=2.0" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
442 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
443 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
444 <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
445 <param name="selected_estimator" value="AdaBoostClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
446 <output name="outfile" file="pipeline07" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
447 </test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
448 <test>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
449 <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
450 <param name="component_type" value="FeatureAgglomeration" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
451 <conditional name="FeatureAgglomeration_selector">
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
452 <param name="select_algorithm" value="FeatureAgglomeration" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
453 <param name="text_params" value="n_clusters=3, affinity='euclidean'" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
454 </conditional>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
455 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
456 <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
457 <param name="selected_estimator" value="AdaBoostClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
458 <output name="outfile" file="pipeline08" compare="sim_size" delta="30" />
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
459 </test>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
460 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
461 <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
462 <param name="component_type" value="skrebate" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
463 <conditional name="skrebate_selector">
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
464 <param name="select_algorithm" value="ReliefF" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
465 <param name="text_params" value="n_features_to_select=3, n_neighbors=100" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
466 </conditional>
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
467 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
468 <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
469 <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
470 <output name="outfile" file="pipeline09" compare="sim_size" delta="30" />
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
471 </test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
472 <test>
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
473 <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
474 <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
475 <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
476 <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
477 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
478 </conditional>
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_module" value="ensemble" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
480 <param name="selected_estimator" value="RandomForestClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
481 <output name="outfile" file="pipeline11" compare="sim_size" delta="30" />
3
ddd8c51b7302 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
482 </test>
6
c2bd4fdba005 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
483 <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
484 <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
485 <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
486 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
487 <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
488 <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
489 <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
490 </test>
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
491 <test>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
492 <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
493 <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
494 <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
495 <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
496 <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
497 <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
498 <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
499 <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
500 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
501 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
502 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
503 <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
504 <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
505 <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
506 </conditional>
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
507 </section>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
508 <output name="outfile" file="pipeline12" compare="sim_size" delta="30" />
7
1187a20b7e2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
509 </test>
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
510 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
511 <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
512 <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
513 </conditional>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
514 <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
515 <param name="selected_estimator" value="RandomForestClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
516 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="30" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
517 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
518 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
519 <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
520 <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
521 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
522 <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
523 <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
524 <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
525 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
526 </section>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
527 <output name="outfile" file="pipeline14" compare="sim_size" delta="30" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
528 </test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
529 <test>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
530 <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
531 <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
532 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
533 <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
534 <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
535 <param name="selected_module" value="binarize_target" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
536 <param name="clf_or_regr" value="BinarizeTargetClassifier" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
537 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
538 </conditional>
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
539 </section>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
540 <output name="outfile" file="pipeline15" compare="sim_size" delta="30" />
8
0be40b86763f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
541 </test>
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
542 <test>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
543 <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
544 <param name="component_type" value="preprocessors" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
545 <conditional name="encoder_selection">
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
546 <param name="encoder_type" value="GenomeOneHotEncoder" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
547 <param name="seq_length" value="1000" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
548 <param name="padding" value="True" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
549 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
550 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
551 <section name="final_estimator">
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
552 <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
553 <param name="selected_module" value="custom_estimator" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
554 <param name="c_estimator" value="keras_model02" ftype="zip" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
555 </conditional>
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
556 </section>
18
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 15
diff changeset
557 <output name="outfile" file="pipeline16" compare="sim_size" delta="30" />
10
0c2586a48d0f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
558 </test>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
559 </tests>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
560 <help>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
561 <![CDATA[
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
562 **What it does**
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
563 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"
bgruening
parents: 10
diff changeset
564
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
565 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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parents: 10
diff changeset
566 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"
bgruening
parents: 10
diff changeset
567
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
568 **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"
bgruening
parents: 10
diff changeset
569
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
570 **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"
bgruening
parents: 10
diff changeset
571
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
572 **Custom estimators**
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
573
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
574 - `GenomeOneHotEncoder`_
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
575
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
576 - `ProteinOnehotEncoder`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
577
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
578 - `IRAPSClassifier`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
579
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
580 - `BinarizeTargetClassifier`_
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
581
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
582 - `BinarizeTargetRegressor`_
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
583
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
584 **Output**
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
585
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
586 - Pickled pipeline/estimator object
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
587
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
588 - Hyperparameter of the ojbect (optional)
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
589
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
590
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
591 .. _`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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diff changeset
592 .. _`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
bgruening
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diff changeset
593 .. _`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
bgruening
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594 .. _`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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595 .. _`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
bgruening
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diff changeset
596 .. _`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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597 .. _`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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598 .. _`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
599
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
600 .. _`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
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601 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
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602 .. _`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
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603 .. _`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
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604 .. _`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
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605 .. _`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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606
15
a7a047cf36d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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607 .. _`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"
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608 .. _`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"
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609 .. _`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"
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610 .. _`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"
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611 .. _`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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612
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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613 ]]>
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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614 </help>
4
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615 <expand macro="sklearn_citation">
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616 <expand macro="skrebate_citation" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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617 <expand macro="xgboost_citation" />
449bd57f70f4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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618 <expand macro="imblearn_citation" />
4
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619 </expand>
0
f8b431b981fa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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620 </tool>