Mercurial > repos > bgruening > sklearn_searchcv

annotate search_model_validation.xml @ 19:006db575e1f3 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
author bgruening
date Sat, 01 May 2021 00:33:20 +0000
parents 92306e3b046c
children 3957f8a3ceae
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1 <tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@" profile="20.05">
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2 <description>performs hyperparameter optimization using various SearchCVs</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 <macro name="search_cv_estimator">
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6 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/>
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7 <param name="is_deep_learning" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Is the estimator a deep learning model?"/>
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8 <section name="search_params_builder" title="Search parameters Builder" expanded="true">
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9 <param name="infile_params" type="data" format="tabular" optional="true" label="Choose the dataset containing parameter names" help="This dataset could be the output of `get_params` in the `Estimator Attributes` tool."/>
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10 <repeat name="param_set" min="1" max="30" title="Parameter settings for search:">
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11 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)">
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12 <options from_dataset="infile_params" startswith="@">
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13 <column name="name" index="2"/>
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14 <column name="value" index="1"/>
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15 <filter type="unique_value" name="unique_param" column="1"/>
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16 </options>
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17 </param>
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18 <param name="sp_list" type="text" value="" optional="true" label="Search list" help="list or array-like, for example: [1, 10, 100, 1000], [True, False] and ['auto', 'sqrt', None]. See `help` section for more examples">
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19 <sanitizer>
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20 <valid initial="default">
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21 <add value="&apos;"/>
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22 <add value="&quot;"/>
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23 <add value="["/>
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24 <add value="]"/>
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25 </valid>
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26 </sanitizer>
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27 </param>
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28 </repeat>
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29 </section>
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30 </macro>
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31 </macros>
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32 <expand macro="python_requirements"/>
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33 <expand macro="macro_stdio"/>
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34 <version_command>echo "@VERSION@"</version_command>
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35 <command><![CDATA[
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36 export HDF5_USE_FILE_LOCKING='FALSE';
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37 #if $input_options.selected_input == 'refseq_and_interval'
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38 bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' &&
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39 tabix -p bed '${target_file.element_identifier}.gz' &&
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40 #end if
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41 python '$__tool_directory__/search_model_validation.py'
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42 --inputs '$inputs'
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43 --estimator '$search_schemes.infile_estimator'
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44 #if $input_options.selected_input == 'seq_fasta'
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45 --fasta_path '$input_options.fasta_path'
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46 #elif $input_options.selected_input == 'refseq_and_interval'
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47 --ref_seq '$input_options.ref_genome_file'
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48 --interval '$input_options.interval_file'
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49 --targets "`pwd`/${target_file.element_identifier}.gz"
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50 #else
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51 --infile1 '$input_options.infile1'
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52 #end if
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53 --infile2 '$input_options.infile2'
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54 #if $save != 'save_no_fit'
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55 --outfile_result '$outfile_result'
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56 #end if
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57 #if $save == 'save_estimator'
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58 --outfile_object '$outfile_object'
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59 #end if
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60 #if $save == 'save_no_fit'
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61 --outfile_object '$outfile_object_no_fit'
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62 #end if
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63 #if $search_schemes.is_deep_learning == 'booltrue' and $save == 'save_estimator' and $outer_split.split_mode == 'nested_cv'
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64 --outfile_weights '$outfile_weights'
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65 #end if
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66 #if $search_schemes.options.cv_selector.selected_cv in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']
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67 --groups '$search_schemes.options.cv_selector.groups_selector.infile_g'
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68 #end if
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69 ]]>
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70 </command>
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71 <configfiles>
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72 <inputs name="inputs" />
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73 </configfiles>
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74 <inputs>
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75 <conditional name="search_schemes">
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76 <param name="selected_search_scheme" type="select" label="Select a model selection search scheme">
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77 <option value="GridSearchCV" selected="true">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option>
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78 <option value="RandomizedSearchCV">RandomizedSearchCV - Randomized search on hyper parameters for an estimator</option>
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79 </param>
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80 <when value="GridSearchCV">
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81 <expand macro="search_cv_estimator"/>
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82 <section name="options" title="Advanced Options for SearchCV" expanded="false">
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83 <expand macro="search_cv_options"/>
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84 </section>
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85 </when>
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86 <when value="RandomizedSearchCV">
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87 <expand macro="search_cv_estimator"/>
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88 <section name="options" title="Advanced Options for SearchCV" expanded="false">
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89 <expand macro="search_cv_options"/>
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90 <param argument="n_iter" type="integer" value="10" label="Number of parameter settings that are sampled"/>
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91 <expand macro="random_state"/>
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92 </section>
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93 </when>
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94 </conditional>
12
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95 <expand macro="sl_mixed_input_plus_sequence"/>
10
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96 <conditional name="outer_split">
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97 <param name="split_mode" type="select" label="Whether to hold a portion of samples for test exclusively?" help="Nested CV or train_test_split">
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98 <option value="no" selected="true">Nope</option>
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99 <option value="nested_cv">Yes - do nested CV</option>
8
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100 </param>
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101 <when value='no'/>
10
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102 <when value="nested_cv">
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103 <expand macro="cv_reduced" label="Select the outer cv splitter"/>
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104 </when>
8
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105 </conditional>
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106 <param name="save" type="select" label="Save best estimator?" help="For a non-deep learning model, save will output fitted best_estimator_ (refit must be true) or a list of cv_results_ from each outer split in nested CV mode. For a deep learning model, by checking the boolean option below the model input, the outputs are two parts, model skeleton and weights. Save Deep learning model for nested CV is not supported.">
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107 <option value="nope">Nope, save is unnecessary</option>
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108 <option value="save_estimator" selected="true">Fitted best estimator or Detailed cv_results_ from nested CV</option>
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109 <option value="save_no_fit">SearchCV object without fitting</option>
10
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110 </param>
0
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111 </inputs>
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112 <outputs>
15
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113 <data format="tabular" name="outfile_result">
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114 <filter>save != 'save_no_fit'</filter>
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115 </data>
10
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116 <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
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117 <filter>save == 'save_estimator' and outer_split['split_mode'] == 'no'</filter>
10
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118 </data>
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119 <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
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120 <filter>search_schemes['is_deep_learning'] and save == 'save_estimator' and outer_split['split_mode'] == 'no'</filter>
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121 </data>
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122 <collection type="list" name="outfile_in_splits" label="cv_results_ from splits on ${on_string}">
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123 <filter>not search_schemes['is_deep_learning'] and save == 'save_estimator' and outer_split['split_mode'] == 'nested_cv'</filter>
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124 <discover_datasets format="tabular" pattern="__name__" directory="cv_results_in_folds"/>
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125 </collection>
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126 <data format="zip" name="outfile_object_no_fit" label="Unfitted SearchCV on ${on_string}">
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127 <filter>save == 'save_no_fit'</filter>
0
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128 </data>
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129 </outputs>
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130 <tests>
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131 <test>
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132 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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133 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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134 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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135 <repeat name="param_set">
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136 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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137 <param name="sp_name" value="svr__C"/>
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138 </repeat>
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139 <repeat name="param_set">
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140 <param name="sp_list" value="[-1, 3, 5, 7, 9]"/>
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141 <param name="sp_name" value="selectkbest__k"/>
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142 </repeat>
3
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143 <param name="error_score" value="false"/>
0
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144 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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145 <param name="header1" value="true" />
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146 <param name="selected_column_selector_option" value="all_columns"/>
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147 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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148 <param name="header2" value="true" />
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149 <param name="selected_column_selector_option2" value="all_columns"/>
5
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150 <output name="outfile_result">
0
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151 <assert_contents>
5
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152 <has_n_columns n="13"/>
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153 <has_text text="0.7938837807353147"/>
8
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154 <has_text text="{'selectkbest__k': 9, 'svr__C': 1}"/>
0
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155 </assert_contents>
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156 </output>
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157 </test>
5
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158 <test expect_failure="true">
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159 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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160 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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161 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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162 <repeat name="param_set">
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163 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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164 <param name="sp_name" value="svr__C"/>
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165 </repeat>
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166 <repeat name="param_set">
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167 <param name="sp_list" value="[-1, 3, 5, 7, 9]"/>
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168 <param name="sp_name" value="selectkbest__k"/>
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169 </repeat>
5
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170 <param name="error_score" value="true"/>
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171 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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172 <param name="header1" value="true" />
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173 <param name="selected_column_selector_option" value="all_columns"/>
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174 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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175 <param name="header2" value="true" />
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176 <param name="selected_column_selector_option2" value="all_columns"/>
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177 </test>
0
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178 <test>
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179 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
8
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180 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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181 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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182 <repeat name="param_set">
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183 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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184 <param name="sp_name" value="svr__C"/>
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185 </repeat>
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186 <repeat name="param_set">
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187 <param name="sp_list" value="['linear', 'poly', 'rbf', 'sigmoid']"/>
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188 <param name="sp_name" value="svr__kernel"/>
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189 </repeat>
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190 <repeat name="param_set">
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191 <param name="sp_list" value="[3, 5, 7, 9]"/>
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192 <param name="sp_name" value="selectkbest__k"/>
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193 </repeat>
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194 <repeat name="param_set">
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195 <param name="sp_list" value="[True, False]"/>
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196 <param name="sp_name" value="robustscaler__with_centering"/>
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197 </repeat>
0
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198 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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199 <param name="header1" value="true" />
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200 <param name="selected_column_selector_option" value="all_columns"/>
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201 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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202 <param name="header2" value="true" />
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203 <param name="selected_column_selector_option2" value="all_columns"/>
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204 <output name="outfile_result" >
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205 <assert_contents>
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206 <has_n_columns n="15" />
8
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207 <has_text text="param_robustscaler__with_centering"/>
0
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208 </assert_contents>
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209 </output>
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210 </test>
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211 <test>
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212 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
8
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213 <param name="infile_estimator" value="pipeline03" ftype="zip"/>
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214 <param name="infile_params" value="get_params03.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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215 <repeat name="param_set">
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216 <param name="sp_list" value="np_arange(50, 1001, 50)"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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217 <param name="sp_name" value="xgbclassifier__n_estimators"/>
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218 </repeat>
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219 <repeat name="param_set">
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220 <param name="sp_list" value="scipy_stats_randint(1, 51)"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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221 <param name="sp_name" value="xgbclassifier__max_depth"/>
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222 </repeat>
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223 <repeat name="param_set">
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224 <param name="sp_list" value="scipy_stats_uniform(0., 1.)"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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225 <param name="sp_name" value="xgbclassifier__gamma"/>
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226 </repeat>
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227 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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228 <param name="sp_list" value="[324089]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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229 <param name="sp_name" value="xgbclassifier__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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230 </repeat>
0
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231 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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232 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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233 <param name="selected_column_selector_option" value="all_columns"/>
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234 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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235 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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236 <param name="selected_column_selector_option2" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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237 <output name="outfile_result" >
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238 <assert_contents>
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239 <has_n_columns n="15" />
8
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240 <has_text text="param_xgbclassifier__max_depth"/>
0
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241 </assert_contents>
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242 </output>
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243 </test>
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244 <test>
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245 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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246 <param name="infile_estimator" value="pipeline04" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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247 <param name="infile_params" value="get_params04.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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248 <repeat name="param_set">
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249 <param name="sp_list" value="list(range(100, 1001, 100))"/>
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250 <param name="sp_name" value="linearsvc__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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251 </repeat>
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252 <repeat name="param_set">
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253 <param name="sp_list" value=": [sklearn_ensemble.ExtraTreesClassifier(n_estimators=100, random_state=324089)]"/>
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254 <param name="sp_name" value="selectfrommodel__estimator"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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255 </repeat>
0
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256 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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257 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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258 <param name="selected_column_selector_option" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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259 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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260 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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261 <param name="selected_column_selector_option2" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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262 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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263 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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264 <has_n_columns n="13"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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265 <has_text text="0.05363984674329502"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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266 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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267 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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268 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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269 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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270 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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271 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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272 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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273 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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274 <param name="sp_list" value="[1, 10, 100, 1000]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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275 <param name="sp_name" value="svr__C"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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276 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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277 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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278 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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279 <param name="selected_column_selector_option" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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280 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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281 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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282 <param name="selected_column_selector_option2" value="all_columns"/>
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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283 <param name="save" value="save_estimator"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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284 <output name="outfile_object" file="searchCV01" compare="sim_size" delta="10"/>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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285 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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286 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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287 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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288 <param name="infile_estimator" value="pipeline06" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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289 <param name="infile_params" value="get_params06.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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290 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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291 <param name="sp_list" value="[10, 50, 200, 1000]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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292 <param name="sp_name" value="adaboostregressor__n_estimators"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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293 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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294 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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295 <param name="sp_list" value="[324089]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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296 <param name="sp_name" value="adaboostregressor__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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297 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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298 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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299 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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300 <param name="selected_column_selector_option" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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301 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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302 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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303 <param name="selected_column_selector_option2" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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304 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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305 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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306 <has_n_columns n="13"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
307 <has_text_matching expression=".+0.7772355090078996" />
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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308 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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309 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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310 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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311 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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312 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
313 <param name="infile_estimator" value="pipeline07" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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314 <param name="infile_params" value="get_params07.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
315 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
316 <param name="sp_list" value="[10, 50, 100, 200]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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317 <param name="sp_name" value="adaboostclassifier__n_estimators"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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318 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
319 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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320 <param name="sp_list" value="[324089]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
321 <param name="sp_name" value="adaboostclassifier__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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322 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
323 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
324 <param name="sp_list" value="[1.0, 2.0]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
325 <param name="sp_name" value="rbfsampler__gamma"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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326 </repeat>
7
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diff changeset
327 <param name='selected_cv' value="default"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
328 <param name="n_splits" value="3"/>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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329 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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330 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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331 <param name="selected_column_selector_option" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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332 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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333 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
334 <param name="selected_column_selector_option2" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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335 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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336 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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337 <has_n_columns n="14"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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338 <has_text_matching expression=".+0.05747126436781609[^/d]" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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339 </assert_contents>
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340 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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341 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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342 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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343 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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344 <param name="infile_estimator" value="pipeline08" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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345 <param name="infile_params" value="get_params08.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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346 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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347 <param name="sp_list" value="[10, 50, 100, 200]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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348 <param name="sp_name" value="adaboostclassifier__n_estimators"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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349 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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350 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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351 <param name="sp_list" value="[324089]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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352 <param name="sp_name" value="adaboostclassifier__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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353 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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354 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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355 <param name="sp_list" value="['ward', 'complete', 'average']"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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356 <param name="sp_name" value="featureagglomeration__linkage"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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357 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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358 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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359 <param name="header1" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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360 <param name="selected_column_selector_option" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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361 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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362 <param name="header2" value="true" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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363 <param name="selected_column_selector_option2" value="all_columns"/>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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364 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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365 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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366 <has_text_matching expression=".+0.08045977011494253[^/w]+10[^/w]" />
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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367 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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368 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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369 </test>
2
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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370 <test>
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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371 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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372 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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373 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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374 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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375 <param name="sp_list" value="[1, 10, 100, 1000]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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376 <param name="sp_name" value="svr__C"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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377 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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378 <param name='selected_cv' value="StratifiedKFold"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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379 <param name="n_splits" value="3"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
380 <param name="shuffle" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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381 <param name="random_state" value="10"/>
2
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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parents: 0
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382 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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383 <param name="header1" value="true" />
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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384 <param name="selected_column_selector_option" value="all_columns"/>
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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385 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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386 <param name="header2" value="true" />
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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387 <param name="selected_column_selector_option2" value="all_columns"/>
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
388 <param name="save" value="save_estimator"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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389 <output name="outfile_object" file="searchCV02" compare="sim_size" delta="10"/>
2
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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390 </test>
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
391 <test>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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392 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
393 <param name="infile_estimator" value="pipeline03" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
394 <param name="infile_params" value="get_params03.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
395 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
396 <param name="sp_list" value="[10, 50, 200, 1000]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
397 <param name="sp_name" value="xgbclassifier__n_estimators"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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398 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
399 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
400 <param name="sp_list" value="[324089]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
401 <param name="sp_name" value="xgbclassifier__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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402 </repeat>
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
403 <param name="primary_scoring" value="balanced_accuracy"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
404 <param name='selected_cv' value="StratifiedKFold"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
405 <param name="n_splits" value="3"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
406 <param name="shuffle" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
407 <param name="random_state" value="10"/>
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
408 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
409 <param name="header1" value="true" />
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
410 <param name="selected_column_selector_option" value="all_columns"/>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
411 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
412 <param name="header2" value="true" />
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
413 <param name="selected_column_selector_option2" value="all_columns"/>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
414 <output name="outfile_result" >
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
415 <assert_contents>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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416 <has_n_columns n="13" />
15
e7d5cd2607a6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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parents: 12
diff changeset
417 <has_text text="0.08719866399898475"/>
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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418 </assert_contents>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
419 </output>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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420 </test>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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parents: 5
diff changeset
421 <test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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parents: 5
diff changeset
422 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
423 <param name="infile_estimator" value="pipeline02" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
424 <param name="infile_params" value="get_params02.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
425 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
426 <param name="sp_list" value="[0.01, 0.001]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
427 <param name="sp_name" value="lassocv__eps"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
428 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
429 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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430 <param name="header1" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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431 <param name="selected_column_selector_option" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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432 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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433 <param name="header2" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
434 <param name="selected_column_selector_option2" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
435 <output name="outfile_result">
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
436 <assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
437 <has_n_columns n="12"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
438 <has_text text="0.776296816136668" />
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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439 </assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
440 </output>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
441 </test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
442 <test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
443 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
444 <param name="infile_estimator" value="pipeline05" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
445 <param name="infile_params" value="get_params05.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
446 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
447 <param name="sp_list" value="[10, 50, 100, 300]"/>
15
e7d5cd2607a6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
448 <param name="sp_name" value="n_estimators"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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449 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
450 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
451 <param name="header1" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
452 <param name="selected_column_selector_option" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
453 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
454 <param name="header2" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
455 <param name="selected_column_selector_option2" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
456 <output name="outfile_result">
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
457 <assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
458 <has_n_columns n="12"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
459 <has_text text="0.8176576686816003" />
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
460 </assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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diff changeset
461 </output>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
462 </test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
463 <test expect_failure="true">
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
464 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
465 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
466 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
467 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
468 <param name="sp_list" value="open('~/.ssh/authorized_keys', 'r').read()"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
469 <param name="sp_name" value="svr__C"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
470 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
471 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
472 <param name="header1" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
473 <param name="selected_column_selector_option" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
474 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
475 <param name="header2" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
476 <param name="selected_column_selector_option2" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
477 </test>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
478 <test>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
479 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
480 <param name="infile_estimator" value="pipeline10" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
481 <param name="infile_params" value="get_params10.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
482 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
483 <param name="sp_list" value=": [sklearn_tree.DecisionTreeRegressor(random_state=0), sklearn_tree.ExtraTreeRegressor(random_state=0)]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
484 <param name="sp_name" value="adaboostregressor__base_estimator"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
485 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
486 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
487 <param name="sp_list" value="[10]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
488 <param name="sp_name" value="adaboostregressor__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
489 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
490 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
491 <param name="header1" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
492 <param name="selected_column_selector_option" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
493 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
494 <param name="header2" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
495 <param name="selected_column_selector_option2" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
496 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
497 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
498 <has_n_columns n="13"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
499 <has_text text="0.8165699136618538"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
500 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
501 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
502 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
503 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
504 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
505 <param name="infile_estimator" value="pipeline09" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
506 <param name="infile_params" value="get_params09.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
507 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
508 <param name="sp_list" value=": [sklearn_feature_selection.SelectKBest(),
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
509 sklearn_feature_selection.VarianceThreshold(), skrebate_ReliefF(), sklearn_preprocessing.RobustScaler()]"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
510 <param name="sp_name" value="relieff"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
511 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
512 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
513 <param name="sp_list" value="[10]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
514 <param name="sp_name" value="randomforestregressor__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
515 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
516 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
517 <param name="header1" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
518 <param name="selected_column_selector_option" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
519 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
520 <param name="header2" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
521 <param name="selected_column_selector_option2" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
522 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
523 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
524 <has_n_columns n="13"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
525 <has_text text="0.8151250518677202"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
526 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
527 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
528 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
529 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
530 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
531 <param name="infile_estimator" value="pipeline09" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
532 <param name="infile_params" value="get_params09.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
533 <repeat name="param_set">
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 8
diff changeset
534 <param name="sp_list" value=": [None,'sk_prep_all', 7, 13, skrebate_ReliefF(n_features_to_select=12)]"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
535 <param name="sp_name" value="relieff"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
536 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
537 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
538 <param name="sp_list" value="[10]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
539 <param name="sp_name" value="randomforestregressor__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
540 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
541 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
542 <param name="header1" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
543 <param name="selected_column_selector_option" value="all_columns"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
544 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
545 <param name="header2" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
546 <param name="selected_column_selector_option2" value="all_columns"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
547 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
548 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
549 <has_n_columns n="13"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
550 <has_text text="0.8151250518677202"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
551 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
552 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
553 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
554 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
555 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
556 <param name="infile_estimator" value="pipeline11" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
557 <param name="infile_params" value="get_params11.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
558 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
559 <param name="sp_list" value="[3,4,5]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
560 <param name="sp_name" value="editednearestneighbours__n_neighbors"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
561 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
562 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
563 <param name="sp_list" value="[10]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
564 <param name="sp_name" value="editednearestneighbours__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
565 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
566 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
567 <param name="sp_list" value="[10, 50, 100, 500]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
568 <param name="sp_name" value="randomforestclassifier__n_estimators"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
569 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
570 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
571 <param name="sp_list" value="[10]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
572 <param name="sp_name" value="randomforestclassifier__random_state"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
573 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
574 <param name="primary_scoring" value="f1_macro"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
575 <param name="secondary_scoring" value="balanced_accuracy,accuracy"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
576 <param name="n_splits" value="5"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
577 <param name="infile1" value="imblearn_X.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
578 <param name="header1" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
579 <param name="selected_column_selector_option" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
580 <param name="infile2" value="imblearn_y.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
581 <param name="header2" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
582 <param name="selected_column_selector_option2" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
583 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
584 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
585 <has_n_columns n="33"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
586 <has_text text="0.9945648481554453"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
587 <has_text text="0.9988888888888889"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
588 <has_text text="0.998"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
589 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
590 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
591 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
592 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
593 <param name="selected_search_scheme" value="GridSearchCV"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
594 <param name="infile_estimator" value="pipeline12" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
595 <param name="infile_params" value="get_params12.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
596 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
597 <param name="sp_list" value="[10, 100, 200]"/>
15
e7d5cd2607a6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
598 <param name="sp_name" value="estimator__n_estimators"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
599 </repeat>
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600 <repeat name="param_set">
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601 <param name="sp_list" value="[10, None]"/>
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602 <param name="sp_name" value="n_features_to_select"/>
8
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603 </repeat>
7
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diff changeset
604 <param name="primary_scoring" value="r2"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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605 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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606 <param name="header1" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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607 <param name="selected_column_selector_option" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
608 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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609 <param name="header2" value="true" />
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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610 <param name="selected_column_selector_option2" value="all_columns"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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611 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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612 <assert_contents>
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613 <has_n_columns n="13"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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614 <has_text text="0.8149439619875293"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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615 </assert_contents>
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616 </output>
6
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617 </test>
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618 <test>
8
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619 <conditional name="search_schemes">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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620 <param name="selected_search_scheme" value="GridSearchCV"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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621 <param name="infile_estimator" value="pipeline05" ftype="zip"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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622 <section name="search_params_builder">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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623 <param name="infile_params" value="get_params05.tabular" ftype="tabular"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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624 <repeat name="param_set">
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625 <param name="sp_list" value="[10, 50, 100, 300]"/>
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626 <param name="sp_name" value="n_estimators"/>
10
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627 </repeat>
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628 </section>
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629 </conditional>
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630 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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631 <param name="header1" value="true" />
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632 <param name="selected_column_selector_option" value="all_columns"/>
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633 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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634 <param name="header2" value="true" />
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635 <param name="selected_column_selector_option2" value="all_columns"/>
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636 <conditional name="outer_split">
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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637 <param name="split_mode" value="nested_cv"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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638 <conditional name="cv_selector">
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639 <param name='selected_cv' value="KFold"/>
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640 <param name="n_splits" value="3"/>
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641 <param name="shuffle" value="true" />
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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642 <param name="random_state" value="123"/>
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643 </conditional>
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644 </conditional>
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645 <output name="outfile_result">
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646 <assert_contents>
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647 <has_n_columns n="4"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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648 <has_text text="0.8044418936007722" />
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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649 </assert_contents>
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650 </output>
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651 </test>
0
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652 </tests>
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653 <help>
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654 <![CDATA[
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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655 **What it does**
8
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656 Searches optimized parameter settings for an estimator or pipeline through either exhaustive grid cross validation search or Randomized cross validation search.
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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657 please refer to `Scikit-learn model_selection GridSearchCV`_, `Scikit-learn model_selection RandomizedSearchCV`_ and `Tuning hyper-parameters`_.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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658
8
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659 **Return**
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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660
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661 Outputs `cv_results_` from SearchCV in a tabular dataset if no train_test_split, otherwise the test score(s). Besides, Output of the SearchCV object is optional.
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662
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663 **How to choose search patameters grid?**
0
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664
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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665 Please refer to `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and `xgboost`_ for estimator parameters.
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666 Refer to `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_
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667 and `skrebate`_ for parameter in the pre-processing steps.
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668
8
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669 **Search parameter list** can be list, numpy array, or distribution. The evaluation of settings supports operations in Math,
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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670 list comprehension, numpy.arange(np_arange), most numpy.random(e.g., np_random_uniform) and some scipy.stats(e.g., scipy_stats_zipf) classes or functions, and others.
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671
8
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672 Examples:
0
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673
8
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674 - [3, 5, 7, 9]
0
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675
8
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676 - list(range(50, 1001, 50))
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677
8
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678 - np_arange(0.01, 1, 0.1)
0
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679
8
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680 - np_random_choice(list(range(1, 51)) + [None], size=20)
0
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681
8
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682 - scipy_stats_randin(1, 11)
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683
8
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684 **Estimator / Preprocessor search (additional `:` in the front)**::
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685
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
686 : [sklearn_tree.DecisionTreeRegressor(), sklearn_tree.ExtraTreeRegressor()]
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
687
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
688 : [sklearn_feature_selection.SelectKBest(), sklearn_feature_selection.VarianceThreshold(),
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
689 skrebate_ReliefF(), sklearn_preprocessing.RobustScaler()]
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
690
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
691 **Hot number/keyword for preprocessors**::
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
692
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
693 0 sklearn_preprocessing.StandardScaler(copy=True, with_mean=True, with_std=True)
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
694 1 sklearn_preprocessing.Binarizer(copy=True, threshold=0.0)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
695 2 sklearn_preprocessing.MaxAbsScaler(copy=True)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
696 3 sklearn_preprocessing.Normalizer(copy=True, norm='l2')
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
697 4 sklearn_preprocessing.MinMaxScaler(copy=True, feature_range=(0, 1))
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
698 5 sklearn_preprocessing.PolynomialFeatures(degree=2, include_bias=True, interaction_only=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
699 6 sklearn_preprocessing.RobustScaler(copy=True, quantile_range=(25.0, 75.0), with_centering=True, with_scaling=True)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
700 7 sklearn_feature_selection.SelectKBest(k=10, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
701 8 sklearn_feature_selection.GenericUnivariateSelect(mode='percentile', param=1e-05, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
702 9 sklearn_feature_selection.SelectPercentile(percentile=10, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
703 10 sklearn_feature_selection.SelectFpr(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
704 11 sklearn_feature_selection.SelectFdr(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
705 12 sklearn_feature_selection.SelectFwe(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
706 13 sklearn_feature_selection.VarianceThreshold(threshold=0.0)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
707 14 sklearn_decomposition.FactorAnalysis(copy=True, iterated_power=3, max_iter=1000, n_components=None,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
708 noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
709 15 sklearn_decomposition.FastICA(algorithm='parallel', fun='logcosh', fun_args=None,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
710 max_iter=200, n_components=None, random_state=0, tol=0.0001, w_init=None, whiten=True)
10
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diff changeset
711 16 sklearn_decomposition.IncrementalPCA(batch_size=None, copy=True, n_components=None, whiten=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
712 17 sklearn_decomposition.KernelPCA(alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto',
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
713 fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None,
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
714 n_components=None, random_state=0, remove_zero_eig=False, tol=0)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
715 18 sklearn_decomposition.LatentDirichletAllocation(batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
716 learning_method=None, learning_offset=10.0, max_doc_update_iter=100, max_iter=10, mean_change_tol=0.001, n_components=10,
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
717 n_topics=None, perp_tol=0.1, random_state=0, topic_word_prior=None, total_samples=1000000.0, verbose=0)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
718 19 sklearn_decomposition.MiniBatchDictionaryLearning(alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars',
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
719 n_components=None, n_iter=1000, random_state=0, shuffle=True, split_sign=False, transform_algorithm='omp',
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
720 transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
721 20 sklearn_decomposition.MiniBatchSparsePCA(alpha=1, batch_size=3, callback=None, method='lars', n_components=None,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
722 n_iter=100, random_state=0, ridge_alpha=0.01, shuffle=True, verbose=False)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
723 21 sklearn_decomposition.NMF(alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
724 n_components=None, random_state=0, shuffle=False, solver='cd', tol=0.0001, verbose=0)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 8
diff changeset
725 22 sklearn_decomposition.PCA(copy=True, iterated_power='auto', n_components=None, random_state=0, svd_solver='auto', tol=0.0, whiten=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
726 23 sklearn_decomposition.SparsePCA(U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars',
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
727 n_components=None, random_state=0, ridge_alpha=0.01, tol=1e-08, verbose=False)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 8
diff changeset
728 24 sklearn_decomposition.TruncatedSVD(algorithm='randomized', n_components=2, n_iter=5, random_state=0, tol=0.0)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
729 25 sklearn_kernel_approximation.Nystroem(coef0=None, degree=None, gamma=None, kernel='rbf',
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
730 kernel_params=None, n_components=100, random_state=0)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
731 26 sklearn_kernel_approximation.RBFSampler(gamma=1.0, n_components=100, random_state=0)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
732 27 sklearn_kernel_approximation.AdditiveChi2Sampler(sample_interval=None, sample_steps=2)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
733 28 sklearn_kernel_approximation.SkewedChi2Sampler(n_components=100, random_state=0, skewedness=1.0)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
734 29 sklearn_cluster.FeatureAgglomeration(affinity='euclidean', compute_full_tree='auto', connectivity=None,
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
735 linkage='ward', memory=None, n_clusters=2, pooling_func=<function mean at 0x113078ae8>)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
736 30 skrebate_ReliefF(discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
737 31 skrebate_SURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
738 32 skrebate_SURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
739 33 skrebate_MultiSURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
740 34 skrebate_MultiSURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 8
diff changeset
741 'sk_prep_all': All sklearn preprocessing estimators, i.e., 0-6
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
742 'fs_all': All feature_selection estimators, i.e., 7-13
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
743 'decomp_all': All decomposition estimators, i.e., 14-24
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
744 'k_appr_all': All kernel_approximation estimators, i.e., 25-28
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
745 'reb_all': All skrebate estimators, i.e., 30-34
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
746 'all_0': All except the imbalanced-learn samplers, i.e., 0-34
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
747 'imb_all': All imbalanced-learn sampling methods, i.e., 35-53.
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
748 **CAUTION**: Mix of imblearn and other preprocessors may not work.
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
749 None: opt out of preprocessor
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
750
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
751 Support mix (CAUTION: Mix of imblearn and other preprocessors may not work), e.g.::
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
752
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
753 : [None, 'sk_prep_all', 21, 'k_appr_all', sklearn_feature_selection.SelectKBest(k=50)]
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
754
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
755
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
756
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
757 **Whether to do train_test_split?**
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
758
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
759 Please refer to `https://scikit-learn.org/stable/modules/cross_validation.html#cross-validation`_
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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760
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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761
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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762 .. image:: https://scikit-learn.org/stable/_images/grid_search_cross_validation.png
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
763 :height: 300
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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764 :width: 400
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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765
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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766
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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767 .. _`Scikit-learn model_selection GridSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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768 .. _`Scikit-learn model_selection RandomizedSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.RandomizedSearchCV.html
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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769 .. _`Tuning hyper-parameters`: http://scikit-learn.org/stable/modules/grid_search.html
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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770
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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771 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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772 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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773 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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774 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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775 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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776 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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777 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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778
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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779 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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780 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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781 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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782 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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783 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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784 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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785 .. _`https://scikit-learn.org/stable/modules/cross_validation.html#cross-validation`: https://scikit-learn.org/stable/modules/cross_validation.html#cross-validation
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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786
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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787 ]]>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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788 </help>
4
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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789 <expand macro="sklearn_citation">
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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790 <expand macro="skrebate_citation"/>
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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791 <expand macro="xgboost_citation"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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792 <expand macro="imblearn_citation"/>
4
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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793 </expand>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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794 </tool>