Mercurial > repos > bgruening > sklearn_build_pipeline

annotate pipeline.xml @ 15:3f3c6dc38f3e draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author bgruening
date Mon, 16 Dec 2019 05:39:20 -0500
parents 775b004b7920
children 4de3d598c116
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@">
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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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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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87 options = safe_eval( 'dict(' + options + ')' )
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88 obj.set_params(**options)
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89 elif input_json['component_type'] == 'kernel_approximation':
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diff changeset
90 algorithm = input_json['kernel_approximation_selector']['select_algorithm']
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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91 obj = getattr(kernel_approximation, algorithm)()
73535ddcfa69 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 != '':
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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94 options = safe_eval( 'dict(' + options + ')' )
0
73535ddcfa69 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)()
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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99 options = input_json['FeatureAgglomeration_selector']['text_params'].strip()
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100 if options != '':
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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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:
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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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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121 obj = Z_RandomOverSampler()
7
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122 else:
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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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134 try:
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135 params = safe_eval('dict(' + core_params + ')')
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136 except ValueError:
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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137 sys.exit("Unsupported parameter input: `%s`" % core_params)
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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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148 IRAPSClassifier = try_get_attr('galaxy_ml.iraps_classifier','IRAPSClassifier')
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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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156 if 'n_jobs' in obj.get_params():
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157 obj.set_params( n_jobs=N_JOBS )
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158 return obj, is_imblearn
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159
7
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diff changeset
160 has_imblearn = False
0
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161 if len(params['pipeline_component']) == 1:
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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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164 pipeline_steps.append( step_obj )
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165 if is_imblearn:
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166 has_imblearn = True
0
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167 else:
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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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
0
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173
8
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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 = '$final_estimator.estimator_selector.transformer'
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184 #end if
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185 with open(regressor_path, 'rb') as f:
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186 regressor = load_model(f)
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187 with open(transformer_path, 'rb') as f:
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188 transformer = load_model(f)
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189 estimator = compose.TransformedTargetRegressor(regressor=regressor, transformer=transformer)
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190 pipeline_steps.append( estimator )
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191 else:
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192 estimator = get_estimator(estimator_json)
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193 pipeline_steps.append( estimator )
0
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194
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195 if len(pipeline_steps) == 1:
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196 out_obj = pipeline_steps[-1]
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197 print(out_obj)
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198 else:
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199 if has_imblearn:
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200 out_obj = imb_make_pipeline(*pipeline_steps)
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201 else:
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202 out_obj = make_pipeline(*pipeline_steps)
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203 pprint.pprint(out_obj.named_steps)
0
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204
7
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205 with open('$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
0
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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>
0
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230 </param>
3
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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"/>
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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"/>
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246 </when>
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247 <when value="FeatureAgglomeration">
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248 <expand macro="FeatureAgglomeration"/>
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249 </when>
3
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250 <when value="skrebate">
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251 <expand macro="skrebate"/>
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252 </when>
7
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253 <when value="imblearn">
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diff changeset
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"
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258 label="Type in parameter settings for IRAPSCore if different from default:"
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259 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes"/>
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260 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001"/>
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261 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1"/>
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262 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7"/>
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263 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1"/>
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264 </when>
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265 <when value="preprocessors">
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266 <expand macro="preprocessors_sequence_encoders"/>
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267 </when>
0
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268 </conditional>
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269 </repeat>
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270 <section name="final_estimator" title="Final Estimator" expanded="true">
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271 <conditional name="estimator_selector">
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272 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
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273 <expand macro="estimator_module_options">
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274 <option value="sklearn.compose">sklearn.compose</option>
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275 <option value="binarize_target">Binarize Target Classifier or Regressor</option>
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276 <option value="custom_estimator">Load a custom estimator</option>
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277 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option>
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278 </expand>
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279 </param>
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280 <expand macro="estimator_suboptions">
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281 <when value="sklearn.compose">
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282 <param name="selected_estimator" type="select" label="Choose estimator class:">
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283 <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
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284 </param>
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285 <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor"/>
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286 <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer"/>
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287 </when>
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288 <when value="binarize_target">
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289 <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
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290 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
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291 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
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292 </param>
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293 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline"/>
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294 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score"/>
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295 <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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296 <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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297 </when>
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298 <when value="custom_estimator">
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299 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/>
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300 </when>
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301 <when value="none"/>
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302 </expand>
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303 </conditional>
0
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304 </section>
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305 <!--param name="output_type" type="select" label="Output the final estimator instead?">
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306 <option value="Pipeline_Builder" selected="true">Pipeline</option>
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307 <option value="Final_Estimator_Builder">Final Estimator</option>
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308 </param>-->
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309 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?"
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310 help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool."/>
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311 </inputs>
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312 <outputs>
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313 <data format="zip" name="outfile" label="New Pipleline/Estimator"/>
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314 <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator">
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315 <filter>get_params</filter>
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316 </data>
0
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317 </outputs>
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318 <tests>
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319 <test>
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320 <conditional name="component_selector">
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321 <param name="component_type" value="pre_processor"/>
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322 <conditional name="pre_processors">
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323 <param name="selected_pre_processor" value="QuantileTransformer"/>
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324 <section name="options">
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325 <param name="random_state" value="10"/>
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326 </section>
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327 </conditional>
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328 </conditional>
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329 <section name="final_estimator">
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330 <conditional name="estimator_selector">
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331 <param name="selected_module" value="none"/>
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332 </conditional>
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333 </section>
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334 <output name="outfile" file="pipeline17" compare="sim_size" delta="5"/>
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335 </test>
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336 <test>
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337 <conditional name="component_selector">
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338 <param name="component_type" value="pre_processor"/>
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339 <conditional name="pre_processors">
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340 <param name="selected_pre_processor" value="PowerTransformer"/>
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341 </conditional>
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342 </conditional>
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343 <section name="final_estimator">
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344 <conditional name="estimator_selector">
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345 <param name="selected_module" value="sklearn.compose"/>
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346 <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip"/>
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347 <param name="transformer" value="pipeline17" ftype="zip"/>
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348 </conditional>
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349 </section>
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diff changeset
350 <param name="get_params" value="true"/>
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
351 <output name="outfile_params" file="pipeline_params18" ftype="tabular"/>
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
352 </test>
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
353 <test>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
354 <repeat name="pipeline_component">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
355 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
356 <param name="component_type" value="pre_processor"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
357 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
358 <param name="selected_pre_processor" value="RobustScaler"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
359 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
360 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
361 </repeat>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
362 <repeat name="pipeline_component">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
363 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
364 <param name="component_type" value="feature_selection"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
365 <conditional name="fs_algorithm_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
366 <param name="selected_algorithm" value="SelectKBest"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
367 <param name="score_func" value="f_classif"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
368 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
369 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
370 </repeat>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
371 <param name="selected_module" value="svm"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
372 <param name="selected_estimator" value="SVR"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
373 <param name="text_params" value="kernel='linear'"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
374 <output name="outfile" file="pipeline01" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
375 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
376 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
377 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
378 <param name="component_type" value="pre_processor"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
379 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
380 <param name="selected_pre_processor" value="RobustScaler"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
381 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
382 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
383 <param name="selected_module" value="linear_model"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
384 <param name="selected_estimator" value="LassoCV"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
385 <output name="outfile" file="pipeline02" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
386 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
387 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
388 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
389 <param name="component_type" value="pre_processor"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
390 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
391 <param name="selected_pre_processor" value="RobustScaler"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
392 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
393 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
394 <param name="selected_module" value="xgboost"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
395 <param name="selected_estimator" value="XGBClassifier"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
396 <output name="outfile" file="pipeline03" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
397 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
398 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
399 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
400 <param name="component_type" value="feature_selection"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
401 <conditional name="fs_algorithm_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
402 <param name="selected_algorithm" value="SelectFromModel"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
403 <conditional name="model_inputter">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
404 <conditional name="estimator_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
405 <param name="selected_module" value="ensemble"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
406 <param name="selected_estimator" value="AdaBoostClassifier"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
407 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
408 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
409 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
410 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
411 <section name="final_estimator">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
412 <param name="selected_module" value="svm"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
413 <param name="selected_estimator" value="LinearSVC"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
414 </section>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
415 <output name="outfile" file="pipeline04" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
416 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
417 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
418 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
419 <param name="component_type" value="None"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
420 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
421 <param name="selected_module" value="ensemble"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
422 <param name="selected_estimator" value="RandomForestRegressor"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
423 <param name="text_params" value="n_estimators=100, random_state=42"/>
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
424 <param name="get_params" value="true"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
425 <output name="outfile" file="pipeline05" compare="sim_size" delta="5"/>
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 10
diff changeset
426 <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
427 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
428 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
429 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
430 <param name="component_type" value="decomposition"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
431 <conditional name="matrix_decomposition_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
432 <param name="select_algorithm" value="PCA"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
433 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
434 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
435 <param name="selected_module" value="ensemble"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
436 <param name="selected_estimator" value="AdaBoostRegressor"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
437 <output name="outfile" file="pipeline06" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
438 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
439 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
440 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
441 <param name="component_type" value="kernel_approximation"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
442 <conditional name="kernel_approximation_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
443 <param name="select_algorithm" value="RBFSampler"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
444 <param name="text_params" value="n_components=10, gamma=2.0"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
445 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
446 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
447 <param name="selected_module" value="ensemble"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
448 <param name="selected_estimator" value="AdaBoostClassifier"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
449 <output name="outfile" file="pipeline07" compare="sim_size" delta="5"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
450 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
451 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
452 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
453 <param name="component_type" value="FeatureAgglomeration"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
454 <conditional name="FeatureAgglomeration_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
455 <param name="select_algorithm" value="FeatureAgglomeration"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
456 <param name="text_params" value="n_clusters=3, affinity='euclidean'"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
457 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
458 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
459 <param name="selected_module" value="ensemble"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
460 <param name="selected_estimator" value="AdaBoostClassifier"/>
8
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
461 <output name="outfile" file="pipeline08" compare="sim_size" delta="20"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
462 </test>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
463 <test>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
464 <conditional name="component_selector">
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
465 <param name="component_type" value="skrebate"/>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
466 <conditional name="skrebate_selector">
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
467 <param name="select_algorithm" value="ReliefF"/>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
468 <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
469 </conditional>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
470 </conditional>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
471 <param name="selected_module" value="ensemble"/>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
472 <param name="selected_estimator" value="RandomForestRegressor"/>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
473 <output name="outfile" file="pipeline09" compare="sim_size" delta="5"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
474 </test>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
475 <test>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
476 <conditional name="component_selector">
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
477 <param name="component_type" value="imblearn"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
478 <conditional name="imblearn_selector">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
479 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
480 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
481 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
482 <param name="selected_module" value="ensemble"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
483 <param name="selected_estimator" value="RandomForestClassifier"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
484 <output name="outfile" file="pipeline11" compare="sim_size" delta="5"/>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
485 </test>
6
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
486 <test expect_failure="true">
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
487 <conditional name="component_selector">
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
488 <param name="component_type" value="None"/>
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
489 </conditional>
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
490 <param name="selected_module" value="ensemble"/>
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
491 <param name="selected_estimator" value="RandomForestRegressor"/>
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
492 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')"/>
52c4e0ef580a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
493 </test>
7
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
494 <test>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
495 <conditional name="component_selector">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
496 <param name="component_type" value="feature_selection"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
497 <conditional name="fs_algorithm_selector">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
498 <param name="selected_algorithm" value="RFE"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
499 <conditional name="estimator_selector">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
500 <param name="selected_module" value="xgboost"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
501 <param name="selected_estimator" value="XGBRegressor"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
502 <param name="text_params" value="random_state=0"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
503 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
504 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
505 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
506 <section name="final_estimator">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
507 <conditional name="estimator_selector">
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
508 <param name="selected_module" value="none"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
509 </conditional>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
510 </section>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
511 <output name="outfile" file="pipeline12" compare="sim_size" delta="5"/>
99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
512 </test>
8
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
513 <test>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
514 <conditional name="component_selector">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
515 <param name="component_type" value="None"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
516 </conditional>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
517 <param name="selected_module" value="ensemble"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
518 <param name="selected_estimator" value="RandomForestClassifier"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
519 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="5"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
520 </test>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
521 <test>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
522 <conditional name="component_selector">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
523 <param name="component_type" value="IRAPS"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
524 </conditional>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
525 <section name="final_estimator">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
526 <conditional name="estimator_selector">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
527 <param name="selected_module" value="none"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
528 </conditional>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
529 </section>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
530 <output name="outfile" file="pipeline14" compare="sim_size" delta="5"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
531 </test>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
532 <test>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
533 <conditional name="component_selector">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
534 <param name="component_type" value="None"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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535 </conditional>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
536 <section name="final_estimator">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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537 <conditional name="estimator_selector">
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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538 <param name="selected_module" value="binarize_target"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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539 <param name="clf_or_regr" value="BinarizeTargetClassifier"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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540 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
541 </conditional>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
542 </section>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
543 <output name="outfile" file="pipeline15" compare="sim_size" delta="5"/>
913ee94945f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
544 </test>
10
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 8
diff changeset
545 <test>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
546 <conditional name="component_selector">
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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547 <param name="component_type" value="preprocessors"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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548 <conditional name="encoder_selection">
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549 <param name="encoder_type" value="GenomeOneHotEncoder"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
550 <param name="seq_length" value="1000"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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551 <param name="padding" value="True"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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552 </conditional>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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553 </conditional>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
554 <section name="final_estimator">
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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555 <conditional name="estimator_selector">
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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556 <param name="selected_module" value="custom_estimator"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
557 <param name="c_estimator" value="keras_model02" ftype="zip"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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558 </conditional>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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559 </section>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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560 <output name="outfile" file="pipeline16" compare="sim_size" delta="5"/>
775b004b7920 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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561 </test>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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562 </tests>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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563 <help>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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564 <![CDATA[
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
565 **What it does**
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
566 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.
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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567
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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568 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.
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
569 For more information, please refer to `Scikit-learn pipeline Pipeline`_.
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
570
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
571 **Pre-processing components** come from `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_, `skrebate`_ and more.
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
572
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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573 **Final Estimator** supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and so on.
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
574
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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575 **Custom estimators**
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
576
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
577 - `GenomeOneHotEncoder`_
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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578
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
579 - `ProteinOnehotEncoder`_
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
580
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
581 - `IRAPSClassifier`_
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
582
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
583 - `BinarizeTargetClassifier`_
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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584
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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585 - `BinarizeTargetRegressor`_
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
586
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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587 **Output**
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
588
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
589 - Pickled pipeline/estimator object
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
590
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
591 - Hyperparameter of the ojbect (optional)
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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592
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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593
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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594 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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595 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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596 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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597 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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598 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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599 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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600 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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601 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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602
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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603 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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604 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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605 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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606 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
607 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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608 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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609
15
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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610 .. _`GenomeOneHotEncoder`: https://goeckslab.github.io/Galaxy-ML/APIs/preprocessors/#genomeonehotencoder
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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611 .. _`ProteinOnehotEncoder`: https://goeckslab.github.io/Galaxy-ML/APIs/preprocessors/#proteinonehotencoder
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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612 .. _`IRAPSClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/iraps-classifier/#irapsclassifier
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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613 .. _`BinarizeTargetClassifier`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetclassifier
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
614 .. _`BinarizeTargetRegressor`: https://goeckslab.github.io/Galaxy-ML/APIs/binarize-target/#binarizetargetregressor
3f3c6dc38f3e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
615
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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616 ]]>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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617 </help>
4
86450dde8682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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618 <expand macro="sklearn_citation">
86450dde8682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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619 <expand macro="skrebate_citation"/>
86450dde8682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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620 <expand macro="xgboost_citation"/>
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99038af8deda planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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621 <expand macro="imblearn_citation"/>
4
86450dde8682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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622 </expand>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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623 </tool>