Mercurial > repos > bgruening > sklearn_searchcv

annotate search_model_validation.xml @ 16:17b349e8f044 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
author bgruening
date Wed, 22 Jan 2020 12:27:44 +0000
parents e7d5cd2607a6
children 92306e3b046c
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1 <tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@">
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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>
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36 <![CDATA[
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37 export HDF5_USE_FILE_LOCKING='FALSE';
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38 #if $input_options.selected_input == 'refseq_and_interval'
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39 bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' &&
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40 tabix -p bed '${target_file.element_identifier}.gz' &&
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41 #end if
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42 python '$__tool_directory__/search_model_validation.py'
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43 --inputs '$inputs'
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44 --estimator '$search_schemes.infile_estimator'
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45 #if $input_options.selected_input == 'seq_fasta'
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46 --fasta_path '$input_options.fasta_path'
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47 #elif $input_options.selected_input == 'refseq_and_interval'
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48 --ref_seq '$input_options.ref_genome_file'
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49 --interval '$input_options.interval_file'
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50 --targets "`pwd`/${target_file.element_identifier}.gz"
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51 #else
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52 --infile1 '$input_options.infile1'
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53 #end if
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54 --infile2 '$input_options.infile2'
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55 #if $save != 'save_no_fit'
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56 --outfile_result "`pwd`/tmp_outfile_result"
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57 #end if
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58 #if $save == 'save_estimator'
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59 --outfile_object '$outfile_object'
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60 #end if
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61 #if $save == 'save_no_fit'
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62 --outfile_object '$outfile_object_no_fit'
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63 #end if
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64 #if $search_schemes.is_deep_learning == 'booltrue' and $save == 'save_estimator' and $outer_split.split_mode == 'nested_cv'
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65 --outfile_weights '$outfile_weights'
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66 #end if
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67 #if $search_schemes.options.cv_selector.selected_cv in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']
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68 --groups '$search_schemes.options.cv_selector.groups_selector.infile_g'
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69 #end if
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70 #if $save != 'save_no_fit'
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71 >'$outfile_result' && cp '$outfile_result' "`pwd`/../tool_stdout"
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72 && cp "`pwd`/tmp_outfile_result" '$outfile_result';
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73 #end if
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74
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75 ]]>
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76 </command>
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77 <configfiles>
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78 <inputs name="inputs" />
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79 </configfiles>
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80 <inputs>
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81 <conditional name="search_schemes">
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82 <param name="selected_search_scheme" type="select" label="Select a model selection search scheme">
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83 <option value="GridSearchCV" selected="true">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option>
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84 <option value="RandomizedSearchCV">RandomizedSearchCV - Randomized search on hyper parameters for an estimator</option>
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85 </param>
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86 <when value="GridSearchCV">
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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 </section>
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91 </when>
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92 <when value="RandomizedSearchCV">
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93 <expand macro="search_cv_estimator"/>
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94 <section name="options" title="Advanced Options for SearchCV" expanded="false">
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95 <expand macro="search_cv_options"/>
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96 <param argument="n_iter" type="integer" value="10" label="Number of parameter settings that are sampled"/>
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97 <expand macro="random_state"/>
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98 </section>
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99 </when>
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100 </conditional>
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101 <expand macro="sl_mixed_input_plus_sequence"/>
10
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102 <conditional name="outer_split">
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103 <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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104 <option value="no" selected="true">Nope</option>
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105 <option value="nested_cv">Yes - do nested CV</option>
8
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106 </param>
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107 <when value='no'/>
10
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108 <when value="nested_cv">
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109 <expand macro="cv_reduced" label="Select the outer cv splitter"/>
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110 </when>
8
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111 </conditional>
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112 <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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113 <option value="nope">Nope, save is unnecessary</option>
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114 <option value="save_estimator" selected="true">Fitted best estimator or Detailed cv_results_ from nested CV</option>
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115 <option value="save_no_fit">SearchCV object without fitting</option>
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116 </param>
0
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117 </inputs>
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118 <outputs>
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119 <data format="tabular" name="outfile_result">
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120 <filter>save != 'save_no_fit'</filter>
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121 </data>
10
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122 <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
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123 <filter>save == 'save_estimator' and outer_split['split_mode'] == 'no'</filter>
10
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124 </data>
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125 <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
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126 <filter>search_schemes['is_deep_learning'] and save == 'save_estimator' and outer_split['split_mode'] == 'no'</filter>
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127 </data>
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128 <collection type="list" name="outfile_in_splits" label="cv_results_ from splits on ${on_string}">
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129 <filter>not search_schemes['is_deep_learning'] and save == 'save_estimator' and outer_split['split_mode'] == 'nested_cv'</filter>
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130 <discover_datasets format="tabular" pattern="__name__" directory="cv_results_in_folds"/>
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131 </collection>
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132 <data format="zip" name="outfile_object_no_fit" label="Unfitted SearchCV on ${on_string}">
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133 <filter>save == 'save_no_fit'</filter>
0
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134 </data>
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135 </outputs>
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136 <tests>
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137 <test>
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138 <param name="selected_search_scheme" value="GridSearchCV"/>
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139 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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140 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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141 <repeat name="param_set">
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142 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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143 <param name="sp_name" value="svr__C"/>
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144 </repeat>
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145 <repeat name="param_set">
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146 <param name="sp_list" value="[-1, 3, 5, 7, 9]"/>
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147 <param name="sp_name" value="selectkbest__k"/>
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148 </repeat>
3
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149 <param name="error_score" value="false"/>
0
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150 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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151 <param name="header1" value="true" />
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152 <param name="selected_column_selector_option" value="all_columns"/>
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153 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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154 <param name="header2" value="true" />
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155 <param name="selected_column_selector_option2" value="all_columns"/>
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156 <output name="outfile_result">
0
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157 <assert_contents>
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158 <has_n_columns n="13"/>
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159 <has_text text="0.7938837807353147"/>
8
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160 <has_text text="{'selectkbest__k': 9, 'svr__C': 1}"/>
0
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161 </assert_contents>
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162 </output>
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163 </test>
5
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164 <test expect_failure="true">
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165 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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166 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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167 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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168 <repeat name="param_set">
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169 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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170 <param name="sp_name" value="svr__C"/>
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171 </repeat>
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172 <repeat name="param_set">
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173 <param name="sp_list" value="[-1, 3, 5, 7, 9]"/>
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174 <param name="sp_name" value="selectkbest__k"/>
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175 </repeat>
5
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176 <param name="error_score" value="true"/>
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177 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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178 <param name="header1" value="true" />
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179 <param name="selected_column_selector_option" value="all_columns"/>
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180 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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181 <param name="header2" value="true" />
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182 <param name="selected_column_selector_option2" value="all_columns"/>
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183 </test>
0
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184 <test>
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185 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
8
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186 <param name="infile_estimator" value="pipeline01" ftype="zip"/>
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187 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
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188 <repeat name="param_set">
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189 <param name="sp_list" value="[1, 10, 100, 1000]"/>
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190 <param name="sp_name" value="svr__C"/>
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191 </repeat>
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192 <repeat name="param_set">
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193 <param name="sp_list" value="['linear', 'poly', 'rbf', 'sigmoid']"/>
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194 <param name="sp_name" value="svr__kernel"/>
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195 </repeat>
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196 <repeat name="param_set">
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197 <param name="sp_list" value="[3, 5, 7, 9]"/>
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198 <param name="sp_name" value="selectkbest__k"/>
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199 </repeat>
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200 <repeat name="param_set">
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201 <param name="sp_list" value="[True, False]"/>
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202 <param name="sp_name" value="robustscaler__with_centering"/>
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203 </repeat>
0
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204 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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205 <param name="header1" value="true" />
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206 <param name="selected_column_selector_option" value="all_columns"/>
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207 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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208 <param name="header2" value="true" />
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209 <param name="selected_column_selector_option2" value="all_columns"/>
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210 <output name="outfile_result" >
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211 <assert_contents>
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212 <has_n_columns n="15" />
8
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213 <has_text text="param_robustscaler__with_centering"/>
0
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214 </assert_contents>
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215 </output>
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216 </test>
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217 <test>
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218 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
8
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219 <param name="infile_estimator" value="pipeline03" ftype="zip"/>
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220 <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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221 <repeat name="param_set">
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222 <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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223 <param name="sp_name" value="xgbclassifier__n_estimators"/>
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224 </repeat>
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225 <repeat name="param_set">
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226 <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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227 <param name="sp_name" value="xgbclassifier__max_depth"/>
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228 </repeat>
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229 <repeat name="param_set">
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230 <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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231 <param name="sp_name" value="xgbclassifier__gamma"/>
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232 </repeat>
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233 <repeat name="param_set">
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234 <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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235 <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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236 </repeat>
0
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237 <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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238 <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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239 <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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240 <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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241 <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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242 <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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243 <output name="outfile_result" >
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244 <assert_contents>
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245 <has_n_columns n="15" />
8
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246 <has_text text="param_xgbclassifier__max_depth"/>
0
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247 </assert_contents>
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248 </output>
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249 </test>
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250 <test>
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251 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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252 <param name="infile_estimator" value="pipeline04" ftype="zip"/>
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253 <param name="infile_params" value="get_params04.tabular" ftype="tabular"/>
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254 <repeat name="param_set">
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255 <param name="sp_list" value="list(range(100, 1001, 100))"/>
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256 <param name="sp_name" value="linearsvc__random_state"/>
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257 </repeat>
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258 <repeat name="param_set">
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259 <param name="sp_list" value=": [sklearn_ensemble.ExtraTreesClassifier(n_estimators=100, random_state=324089)]"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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260 <param name="sp_name" value="selectfrommodel__estimator"/>
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261 </repeat>
0
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262 <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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263 <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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264 <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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265 <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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266 <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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267 <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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268 <output name="outfile_result">
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269 <assert_contents>
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270 <has_n_columns n="13"/>
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271 <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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272 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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273 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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274 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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275 <test>
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276 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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277 <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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278 <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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279 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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280 <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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281 <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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282 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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283 <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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284 <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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285 <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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286 <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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287 <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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288 <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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289 <param name="save" value="save_estimator"/>
8
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290 <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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291 </test>
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292 <test>
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293 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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294 <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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295 <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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296 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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297 <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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298 <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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299 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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300 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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301 <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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302 <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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303 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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304 <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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305 <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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306 <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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307 <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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308 <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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309 <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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310 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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311 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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312 <has_n_columns n="13"/>
7
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313 <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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314 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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315 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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316 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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317 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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318 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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319 <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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320 <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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321 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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322 <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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323 <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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324 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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325 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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326 <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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327 <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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328 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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329 <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
330 <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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331 <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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332 </repeat>
7
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333 <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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334 <param name="n_splits" value="3"/>
0
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335 <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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336 <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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337 <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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338 <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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339 <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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340 <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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341 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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342 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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343 <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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344 <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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345 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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346 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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347 </test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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348 <test>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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349 <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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350 <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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351 <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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352 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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353 <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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354 <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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355 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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356 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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357 <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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358 <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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359 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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360 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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361 <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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362 <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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363 </repeat>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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364 <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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365 <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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366 <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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367 <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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368 <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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369 <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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370 <output name="outfile_result">
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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371 <assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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372 <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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373 </assert_contents>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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374 </output>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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375 </test>
2
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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376 <test>
79f41472b53f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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377 <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
378 <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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379 <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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diff changeset
380 <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
381 <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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diff changeset
382 <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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383 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
384 <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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diff changeset
385 <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
386 <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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387 <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
diff changeset
388 <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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diff changeset
389 <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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diff changeset
390 <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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diff changeset
391 <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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diff changeset
392 <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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diff changeset
393 <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
394 <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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diff changeset
395 <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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396 </test>
3
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
397 <test>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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398 <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
399 <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
400 <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
401 <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
402 <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
403 <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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diff changeset
404 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
405 <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
406 <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
407 <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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diff changeset
408 </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
409 <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
410 <param name='selected_cv' value="StratifiedKFold"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
411 <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
412 <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
413 <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
414 <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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parents: 2
diff changeset
415 <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
416 <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
bgruening
parents: 2
diff changeset
417 <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
418 <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
419 <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
420 <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
421 <assert_contents>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
422 <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
423 <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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diff changeset
424 </assert_contents>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
425 </output>
a58ad596036f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
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426 </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
427 <test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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428 <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
429 <param name="infile_estimator" value="pipeline02" 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
430 <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
bgruening
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431 <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
432 <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
433 <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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434 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
435 <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
436 <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
437 <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
438 <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
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439 <param name="header2" value="true" />
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
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440 <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
441 <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
442 <assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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443 <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
444 <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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445 </assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
446 </output>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
447 </test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
448 <test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
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diff changeset
449 <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
450 <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
parents: 7
diff changeset
451 <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
452 <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
453 <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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parents: 12
diff changeset
454 <param name="sp_name" value="n_estimators"/>
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
455 </repeat>
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
456 <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
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
464 <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
465 <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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parents: 5
diff changeset
466 </assert_contents>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
467 </output>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
468 </test>
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
469 <test expect_failure="true">
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
470 <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
471 <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
parents: 7
diff changeset
472 <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
473 <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
474 <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
parents: 7
diff changeset
475 <param name="sp_name" value="svr__C"/>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
476 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
477 <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
478 <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
479 <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
480 <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
481 <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
482 <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
483 </test>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
484 <test>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
485 <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
486 <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
parents: 7
diff changeset
487 <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
parents: 7
diff changeset
488 <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
489 <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
490 <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
parents: 7
diff changeset
491 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
492 <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
493 <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
494 <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
495 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
496 <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
497 <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
498 <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
499 <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
500 <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
501 <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
502 <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
503 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
504 <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
505 <has_text text="0.8165699136618538"/>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
506 </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
507 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
508 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
509 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
510 <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
511 <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
512 <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
513 <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
514 <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
bgruening
parents: 6
diff changeset
515 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
bgruening
parents: 7
diff changeset
516 <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
517 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
518 <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
519 <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
520 <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
521 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
522 <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
523 <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
524 <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
525 <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
526 <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
527 <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
528 <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
529 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
530 <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
531 <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
532 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
533 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
534 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
535 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
536 <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
537 <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
538 <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
539 <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
540 <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
541 <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
542 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
543 <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
544 <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
545 <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
546 </repeat>
6
d4083bfe27d2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
547 <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
548 <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
549 <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
550 <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
551 <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
552 <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
553 <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
554 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
555 <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
556 <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
557 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
558 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
559 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
560 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
561 <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
562 <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
563 <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
564 <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
565 <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
566 <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
567 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
568 <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
569 <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
570 <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
571 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
572 <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
573 <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
574 <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
575 </repeat>
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
576 <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
577 <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
578 <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
579 </repeat>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
580 <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
581 <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
582 <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
583 <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
584 <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
585 <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
586 <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
587 <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
588 <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
589 <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
590 <assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
591 <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
592 <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
593 <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
594 <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
595 </assert_contents>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
596 </output>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
597 </test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
598 <test>
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
599 <param name="selected_search_scheme" value="GridSearchCV"/>
8
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600 <param name="infile_estimator" value="pipeline12" ftype="zip"/>
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601 <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
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diff changeset
602 <repeat name="param_set">
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603 <param name="sp_list" value="[10, 100, 200]"/>
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diff changeset
604 <param name="sp_name" value="estimator__n_estimators"/>
8
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605 </repeat>
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606 <repeat name="param_set">
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607 <param name="sp_list" value="[10, None]"/>
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diff changeset
608 <param name="sp_name" value="n_features_to_select"/>
8
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diff changeset
609 </repeat>
7
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diff changeset
610 <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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611 <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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612 <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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diff changeset
613 <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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614 <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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615 <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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616 <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
617 <output name="outfile_result">
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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618 <assert_contents>
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619 <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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620 <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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621 </assert_contents>
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622 </output>
6
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623 </test>
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624 <test>
8
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diff changeset
625 <conditional name="search_schemes">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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626 <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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627 <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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628 <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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629 <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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630 <repeat name="param_set">
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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631 <param name="sp_list" value="[10, 50, 100, 300]"/>
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632 <param name="sp_name" value="n_estimators"/>
10
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633 </repeat>
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634 </section>
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635 </conditional>
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636 <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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637 <param name="header1" value="true" />
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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638 <param name="selected_column_selector_option" value="all_columns"/>
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639 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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640 <param name="header2" value="true" />
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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641 <param name="selected_column_selector_option2" value="all_columns"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
642 <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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643 <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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644 <conditional name="cv_selector">
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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645 <param name='selected_cv' value="KFold"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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646 <param name="n_splits" value="3"/>
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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647 <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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648 <param name="random_state" value="123"/>
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649 </conditional>
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650 </conditional>
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651 <output name="outfile_result">
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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652 <assert_contents>
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653 <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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654 <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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655 </assert_contents>
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656 </output>
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657 </test>
0
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658 </tests>
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659 <help>
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660 <![CDATA[
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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661 **What it does**
8
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662 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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663 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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664
8
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665 **Return**
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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666
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667 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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668
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669 **How to choose search patameters grid?**
0
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670
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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671 Please refer to `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and `xgboost`_ for estimator parameters.
8
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672 Refer to `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_
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673 and `skrebate`_ for parameter in the pre-processing steps.
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674
8
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675 **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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676 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.
0
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677
8
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678 Examples:
0
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679
8
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680 - [3, 5, 7, 9]
0
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681
8
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682 - list(range(50, 1001, 50))
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683
8
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684 - np_arange(0.01, 1, 0.1)
0
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diff changeset
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 - np_random_choice(list(range(1, 51)) + [None], size=20)
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
687
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
688 - scipy_stats_randin(1, 11)
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
689
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
690 **Estimator / Preprocessor search (additional `:` in the front)**::
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
691
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
692 : [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
693
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
694 : [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
695 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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parents: 6
diff changeset
696
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
697 **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
698
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
699 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
700 1 sklearn_preprocessing.Binarizer(copy=True, threshold=0.0)
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422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
701 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
702 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
703 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
704 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
705 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
706 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
707 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
708 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
709 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
710 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
711 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
712 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
713 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
714 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
715 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
716 max_iter=200, n_components=None, random_state=0, tol=0.0001, w_init=None, whiten=True)
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
717 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
718 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
719 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
bgruening
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diff changeset
720 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
721 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
722 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
723 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
724 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
725 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
726 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
727 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
bgruening
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diff changeset
728 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
729 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
parents: 6
diff changeset
730 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
731 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
732 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
parents: 6
diff changeset
733 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
734 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
735 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
parents: 6
diff changeset
736 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
737 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
738 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
739 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
740 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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parents: 6
diff changeset
741 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
742 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
743 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
744 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
745 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
746 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
747 '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
748 '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
749 '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
750 '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
751 '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
752 '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
753 '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
754 **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
755 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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diff changeset
756
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
757 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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parents: 6
diff changeset
758
10
422f6e8a492d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
759 : [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
760
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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761
8
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
762
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
763 **Whether to do train_test_split?**
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
764
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
765 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
bgruening
parents: 7
diff changeset
766
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
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767
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
768 .. 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
bgruening
parents: 7
diff changeset
769 :height: 300
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
770 :width: 400
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
771
51cabe6d4ca6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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772
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
773 .. _`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
bgruening
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774 .. _`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
bgruening
parents:
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775 .. _`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
bgruening
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776
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
777 .. _`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
bgruening
parents:
diff changeset
778 .. _`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
bgruening
parents:
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779 .. _`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
bgruening
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780 .. _`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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781 .. _`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
bgruening
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782 .. _`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
bgruening
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783 .. _`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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784
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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785 .. _`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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786 .. _`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
bgruening
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787 .. _`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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788 .. _`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
bgruening
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diff changeset
789 .. _`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
bgruening
parents: 2
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790 .. _`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
bgruening
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diff changeset
791 .. _`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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792
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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793 ]]>
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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794 </help>
4
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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diff changeset
795 <expand macro="sklearn_citation">
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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796 <expand macro="skrebate_citation"/>
924af5cfe4c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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797 <expand macro="xgboost_citation"/>
7
bd2ef98a56be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
798 <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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diff changeset
799 </expand>
0
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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800 </tool>