annotate pipeline.xml @ 5:242ca5bcd403 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
author bgruening
date Sat, 29 Sep 2018 07:27:12 -0400
parents 86450dde8682
children 52c4e0ef580a
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@">
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2 <description>constructs a list of transforms and a final estimator</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
3
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6 <expand macro="python_requirements">
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7 <requirement type="package" version="0.6">skrebate</requirement>
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8 </expand>
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9 <expand macro="macro_stdio"/>
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10 <version_command>echo "@VERSION@"</version_command>
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11 <command>
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12 <![CDATA[
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13 python "$sklearn_pipeline_script" '$inputs'
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <inputs name="inputs" />
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18 <configfile name="sklearn_pipeline_script">
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19 <![CDATA[
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20 import sys
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21 import os
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22 import json
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23 import pprint
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24 import skrebate
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25 from sklearn import (preprocessing, svm, linear_model, ensemble, naive_bayes,
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26 tree, neighbors, decomposition, kernel_approximation, cluster)
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27 from sklearn.pipeline import Pipeline
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28
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29 exec(open("$__tool_directory__/utils.py").read(), globals())
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31 safe_eval = SafeEval()
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33 input_json_path = sys.argv[1]
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34 with open(input_json_path, "r") as param_handler:
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35 params = json.load(param_handler)
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36
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37 pipeline_steps = []
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38
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39 def get_component(input_json, check_none=False):
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40 if input_json['component_type'] == 'None':
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41 if not check_none:
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42 return
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43 else:
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44 sys.exit("The pre-processing component type can't be None when the number of components is greater than 1.")
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45 if input_json['component_type'] == 'pre_processor':
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46 preprocessor = input_json["pre_processors"]["selected_pre_processor"]
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47 pre_processor_options = input_json["pre_processors"]["options"]
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48 my_class = getattr(preprocessing, preprocessor)
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49 obj = my_class(**pre_processor_options)
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50 elif input_json['component_type'] == 'feature_selection':
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51 obj = feature_selector(input_json['fs_algorithm_selector'])
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52 elif input_json['component_type'] == 'decomposition':
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53 algorithm = input_json['matrix_decomposition_selector']['select_algorithm']
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54 obj = getattr(decomposition, algorithm)()
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55 options = input_json['matrix_decomposition_selector']['text_params'].strip()
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56 if options != "":
3
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57 options = safe_eval('dict(' + options + ')')
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58 obj.set_params(**options)
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59 elif input_json['component_type'] == 'kernel_approximation':
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60 algorithm = input_json['kernel_approximation_selector']['select_algorithm']
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61 obj = getattr(kernel_approximation, algorithm)()
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62 options = input_json['kernel_approximation_selector']['text_params'].strip()
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63 if options != "":
3
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64 options = safe_eval('dict(' + options + ')')
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65 obj.set_params(**options)
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66 elif input_json['component_type'] == 'FeatureAgglomeration':
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67 algorithm = input_json['FeatureAgglomeration_selector']['select_algorithm']
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68 obj = getattr(cluster, algorithm)()
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69 options = input_json['FeatureAgglomeration_selector']['text_params'].strip()
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70 if options != "":
3
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71 options = safe_eval('dict(' + options + ')')
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72 obj.set_params(**options)
3
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73 elif input_json['component_type'] == 'skrebate':
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74 algorithm = input_json['skrebate_selector']['select_algorithm']
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75 if algorithm == 'TuRF':
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76 obj = getattr(skrebate, algorithm)(core_algorithm='ReliefF')
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77 else:
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78 obj = getattr(skrebate, algorithm)()
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79 options = input_json['skrebate_selector']['text_params'].strip()
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80 if options != "":
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81 options = safe_eval('dict(' + options + ')')
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82 obj.set_params(**options)
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83 if 'n_jobs' in obj.get_params():
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84 obj.set_params( n_jobs=N_JOBS )
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85 return obj
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86
0
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87 if len(params['pipeline_component']) == 1:
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88 step_obj = get_component( params['pipeline_component'][0]['component_selector'])
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89 if step_obj:
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90 pipeline_steps.append( ('preprocessing_1', step_obj) )
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91 else:
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92 for i, c in enumerate(params['pipeline_component']):
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93 step_obj = get_component( c['component_selector'], check_none=True )
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94 pipeline_steps.append( ('preprocessing_' + str(i+1), step_obj) )
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95
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96 # Set up final estimator and add to pipeline.
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97 estimator_json = params["final_estimator"]['estimator_selector']
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98 estimator = get_estimator(estimator_json)
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99
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100 pipeline_steps.append( ('estimator', estimator) )
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101
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102 pipeline = Pipeline(pipeline_steps)
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103 pprint.pprint(pipeline.named_steps)
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104
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105 with open("$outfile", 'wb') as out_handler:
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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106 pickle.dump(pipeline, out_handler, pickle.HIGHEST_PROTOCOL)
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107
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108 ]]>
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109 </configfile>
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110 </configfiles>
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111 <inputs>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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112 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step">
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113 <conditional name="component_selector">
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114 <param name="component_type" type="select" label="Choose the type of transformation:">
3
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115 <option value="None" selected="true">None</option>
0
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116 <option value="pre_processor">Sklearn Preprocessor</option>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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117 <option value="feature_selection">Feature Selection</option>
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118 <option value="decomposition">Matrix Decomposition</option>
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119 <option value="kernel_approximation">Kernel Approximation</option>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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120 <option value="FeatureAgglomeration">Agglomerate Features</option>
3
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121 <option value="skrebate">Skrebate algorithm</option>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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122 </param>
3
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diff changeset
123 <when value="None"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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124 <when value="pre_processor">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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125 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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126 <expand macro="sparse_preprocessors_ext" />
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127 <expand macro="sparse_preprocessor_options_ext" />
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128 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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129 </when>
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130 <when value="feature_selection">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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131 <expand macro="feature_selection_all">
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132 <expand macro="fs_selectfrommodel_no_prefitted"/>
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133 </expand>
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134 </when>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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135 <when value="decomposition">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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136 <expand macro="matrix_decomposition_all"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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137 </when>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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138 <when value="kernel_approximation">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
139 <expand macro="kernel_approximation_all"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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140 </when>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
141 <when value="FeatureAgglomeration">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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142 <expand macro="FeatureAgglomeration"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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143 </when>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
144 <when value="skrebate">
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
145 <expand macro="skrebate"/>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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146 </when>
0
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147 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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148 </repeat>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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149 <section name="final_estimator" title="Final Estimator" expanded="true">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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150 <expand macro="estimator_selector_all" />
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151 </section>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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152 </inputs>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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153 <outputs>
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154 <data format="zip" name="outfile"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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155 </outputs>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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156 <tests>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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157 <test>
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158 <repeat name="pipeline_component">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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159 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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160 <param name="component_type" value="pre_processor"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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161 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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162 <param name="selected_pre_processor" value="RobustScaler"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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163 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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164 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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165 </repeat>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
166 <repeat name="pipeline_component">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
167 <conditional name="component_selector">
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168 <param name="component_type" value="feature_selection"/>
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169 <conditional name="fs_algorithm_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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170 <param name="selected_algorithm" value="SelectKBest"/>
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171 <param name="score_func" value="f_classif"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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172 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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173 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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174 </repeat>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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175 <param name="selected_module" value="svm"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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176 <param name="selected_estimator" value="SVR"/>
3
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177 <param name="text_params" value="kernel='linear'"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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178 <output name="outfile" file="pipeline01" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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179 </test>
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180 <test>
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181 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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182 <param name="component_type" value="pre_processor"/>
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diff changeset
183 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
184 <param name="selected_pre_processor" value="RobustScaler"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
185 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
186 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
187 <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
188 <param name="selected_estimator" value="LassoCV"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
189 <output name="outfile" file="pipeline02" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
190 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
191 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
192 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
193 <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
194 <conditional name="pre_processors">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
195 <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
196 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
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197 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
198 <param name="selected_module" value="xgboost"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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199 <param name="selected_estimator" value="XGBClassifier"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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200 <output name="outfile" file="pipeline03" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
201 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
202 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
203 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
204 <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
205 <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
206 <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
207 <conditional name="model_inputter">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
208 <conditional name="estimator_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
209 <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
210 <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
211 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
212 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
213 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
214 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
215 <section name="final_estimator">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
216 <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
217 <param name="selected_estimator" value="LinearSVC"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
diff changeset
218 </section>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
219 <output name="outfile" file="pipeline04" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
220 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
221 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
222 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
223 <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
224 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
225 <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
226 <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
227 <param name="text_params" value="n_estimators=100, random_state=42"/>
0
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
228 <output name="outfile" file="pipeline05" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
229 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
230 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
231 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
232 <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
233 <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
234 <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
235 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
236 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
237 <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
238 <param name="selected_estimator" value="AdaBoostRegressor"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
239 <output name="outfile" file="pipeline06" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
240 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
241 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
242 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
243 <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
244 <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
245 <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
246 <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
247 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
248 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
249 <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
250 <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
251 <output name="outfile" file="pipeline07" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
252 </test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
253 <test>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
254 <conditional name="component_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
255 <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
256 <conditional name="FeatureAgglomeration_selector">
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
257 <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
258 <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
259 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
260 </conditional>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
261 <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
262 <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
263 <output name="outfile" file="pipeline08" compare="sim_size" delta="1"/>
73535ddcfa69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
264 </test>
3
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
265 <test>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
266 <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
267 <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
268 <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
269 <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
270 <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
271 </conditional>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
272 </conditional>
0857964e07c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 0
diff changeset
273 <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
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274 <param name="selected_estimator" value="RandomForestRegressor"/>
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275 <output name="outfile" file="pipeline09" compare="sim_size" delta="1"/>
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276 </test>
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277 <test>
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278 <conditional name="component_selector">
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279 <param name="component_type" value="skrebate"/>
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280 <conditional name="skrebate_selector">
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281 <param name="select_algorithm" value="TuRF"/>
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282 <param name="text_params" value=""/>
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283 </conditional>
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284 </conditional>
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285 <param name="selected_module" value="ensemble"/>
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286 <param name="selected_estimator" value="RandomForestRegressor"/>
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287 <output name="outfile" file="pipeline10" compare="sim_size" delta="1"/>
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288 </test>
0
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289 </tests>
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290 <help>
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291 <![CDATA[
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292 **What it does**
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293 Constructs a pipeline that contains a list of transfroms and a final estimator. Pipeline assembles several steps
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294 that can be cross-validated together while setting different parameters.
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295 please refer to `Scikit-learn pipeline Pipeline`_.
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296
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297 **Pre-processing components** allow None, one or a combination of up to 5 transformations from `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_ and/or `skrebate`_.
0
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298
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299 **Estimator** selector supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_ and `neighbors`_.
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300
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301
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302 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html
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303 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
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304 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
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305 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
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306 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
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307 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
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308 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
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309 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
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310
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311 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
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312 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
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313 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
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314 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
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315 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
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316 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
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317
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318 ]]>
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319 </help>
4
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320 <expand macro="sklearn_citation">
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321 <expand macro="skrebate_citation"/>
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322 <expand macro="xgboost_citation"/>
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323 </expand>
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324 </tool>