Mercurial > repos > bgruening > sklearn_searchcv

annotate search_model_validation.xml @ 15:c1ca24a1509d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author bgruening
date Mon, 16 Dec 2019 05:41:39 -0500
parents 103aaea17119
children cb5635e30842
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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}">
15
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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}">
15
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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"/>
8
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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"/>
5
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156 <output name="outfile_result">
0
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157 <assert_contents>
5
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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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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187 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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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" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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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"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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208 <param name="header2" value="true" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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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"/>
1c4a241bef5c 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)"/>
1c4a241bef5c 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)"/>
1c4a241bef5c 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.)"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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))"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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256 <param name="sp_name" value="linearsvc__random_state"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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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)]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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261 </repeat>
0
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262 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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271 <has_text text="0.05363984674329502"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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272 </assert_contents>
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273 </output>
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274 </test>
91bf3f0d7455 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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279 <repeat name="param_set">
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280 <param name="sp_list" value="[1, 10, 100, 1000]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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282 </repeat>
0
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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
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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
91bf3f0d7455 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>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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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"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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296 <repeat name="param_set">
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297 <param name="sp_list" value="[10, 50, 200, 1000]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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299 </repeat>
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300 <repeat name="param_set">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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303 </repeat>
0
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
309 <param name="selected_column_selector_option2" value="all_columns"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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310 <output name="outfile_result">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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311 <assert_contents>
91bf3f0d7455 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
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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314 </assert_contents>
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315 </output>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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316 </test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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317 <test>
91bf3f0d7455 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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321 <repeat name="param_set">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
322 <param name="sp_list" value="[10, 50, 100, 200]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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324 </repeat>
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diff changeset
325 <repeat name="param_set">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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328 </repeat>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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329 <repeat name="param_set">
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diff changeset
330 <param name="sp_list" value="[1.0, 2.0]"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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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diff changeset
333 <param name='selected_cv' value="default"/>
4368259ff821 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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341 <output name="outfile_result">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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342 <assert_contents>
91bf3f0d7455 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"/>
91bf3f0d7455 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]" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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345 </assert_contents>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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346 </output>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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347 </test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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348 <test>
91bf3f0d7455 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
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350 <param name="infile_estimator" value="pipeline08" ftype="zip"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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352 <repeat name="param_set">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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355 </repeat>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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356 <repeat name="param_set">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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359 </repeat>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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360 <repeat name="param_set">
1c4a241bef5c 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']"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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363 </repeat>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
364 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
91bf3f0d7455 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" />
91bf3f0d7455 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"/>
91bf3f0d7455 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"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
368 <param name="header2" value="true" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
369 <param name="selected_column_selector_option2" value="all_columns"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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370 <output name="outfile_result">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
371 <assert_contents>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
372 <has_text_matching expression=".+0.08045977011494253[^/w]+10[^/w]" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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373 </assert_contents>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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374 </output>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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375 </test>
2
907bb0418c9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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parents: 0
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376 <test>
907bb0418c9f 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
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
379 <param name="infile_params" value="get_params01.tabular" ftype="tabular"/>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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383 </repeat>
7
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
387 <param name="random_state" value="10"/>
2
907bb0418c9f 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"/>
907bb0418c9f 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" />
907bb0418c9f 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"/>
907bb0418c9f 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"/>
907bb0418c9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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parents: 0
diff changeset
392 <param name="header2" value="true" />
907bb0418c9f 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
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 8
diff changeset
394 <param name="save" value="save_estimator"/>
8
1c4a241bef5c 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
907bb0418c9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
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396 </test>
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
397 <test>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
398 <param name="selected_search_scheme" value="GridSearchCV"/>
8
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
399 <param name="infile_estimator" value="pipeline03" ftype="zip"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents: 7
diff changeset
401 <repeat name="param_set">
1c4a241bef5c 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]"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
403 <param name="sp_name" value="xgbclassifier__n_estimators"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
404 </repeat>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
405 <repeat name="param_set">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
406 <param name="sp_list" value="[324089]"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
407 <param name="sp_name" value="xgbclassifier__random_state"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
408 </repeat>
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
409 <param name="primary_scoring" value="balanced_accuracy"/>
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
410 <param name='selected_cv' value="StratifiedKFold"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
412 <param name="shuffle" value="true" />
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
413 <param name="random_state" value="10"/>
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
414 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
415 <param name="header1" value="true" />
f9fea8323bcb 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"/>
f9fea8323bcb 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"/>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
418 <param name="header2" value="true" />
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
419 <param name="selected_column_selector_option2" value="all_columns"/>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
420 <output name="outfile_result" >
f9fea8323bcb 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>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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parents: 2
diff changeset
422 <has_n_columns n="13" />
15
c1ca24a1509d "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
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
424 </assert_contents>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
425 </output>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
426 </test>
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
427 <test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
428 <param name="selected_search_scheme" value="GridSearchCV"/>
8
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
430 <param name="infile_params" value="get_params02.tabular" ftype="tabular"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
431 <repeat name="param_set">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
432 <param name="sp_list" value="[0.01, 0.001]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
434 </repeat>
6
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 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"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
439 <param name="header2" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
440 <param name="selected_column_selector_option2" value="all_columns"/>
7509d7059040 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">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
442 <assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
443 <has_n_columns n="12"/>
8
1c4a241bef5c 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
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
445 </assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
446 </output>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
447 </test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
448 <test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
449 <param name="selected_search_scheme" value="GridSearchCV"/>
8
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
453 <param name="sp_list" value="[10, 50, 100, 300]"/>
15
c1ca24a1509d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
454 <param name="sp_name" value="n_estimators"/>
8
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
455 </repeat>
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
456 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 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">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
463 <assert_contents>
7509d7059040 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
4368259ff821 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
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
466 </assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
467 </output>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
468 </test>
7509d7059040 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">
7509d7059040 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
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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">
1c4a241bef5c 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()"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
476 </repeat>
6
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
483 </test>
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
484 <test>
6
7509d7059040 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
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
489 <param name="sp_list" value=": [sklearn_tree.DecisionTreeRegressor(random_state=0), sklearn_tree.ExtraTreeRegressor(random_state=0)]"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
490 <param name="sp_name" value="adaboostregressor__base_estimator"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
491 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
494 <param name="sp_name" value="adaboostregressor__random_state"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
495 </repeat>
7
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
503 <assert_contents>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
506 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
507 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
508 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
509 <test>
4368259ff821 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
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
512 <param name="infile_params" value="get_params09.tabular" ftype="tabular"/>
1c4a241bef5c 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">
1c4a241bef5c 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
4368259ff821 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
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
517 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
521 </repeat>
7
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
529 <assert_contents>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
532 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
533 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
534 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
535 <test>
4368259ff821 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
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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
82b6104d4682 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
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
542 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
546 </repeat>
6
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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"/>
7509d7059040 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"/>
7509d7059040 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" />
7509d7059040 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
4368259ff821 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">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
554 <assert_contents>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
557 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
558 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
559 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
560 <test>
4368259ff821 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
1c4a241bef5c 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"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
567 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
571 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
575 </repeat>
1c4a241bef5c 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">
1c4a241bef5c 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]"/>
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
579 </repeat>
7
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
590 <assert_contents>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
595 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
596 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
597 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
598 <test>
4368259ff821 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
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
600 <param name="infile_estimator" value="pipeline12" ftype="zip"/>
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diff changeset
601 <param name="infile_params" value="get_params12.tabular" ftype="tabular"/>
1c4a241bef5c 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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diff changeset
606 <repeat name="param_set">
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diff changeset
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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parents: 6
diff changeset
610 <param name="primary_scoring" value="r2"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
611 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
612 <param name="header1" value="true" />
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
614 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
4368259ff821 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" />
4368259ff821 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"/>
4368259ff821 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">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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618 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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619 <has_n_columns n="13"/>
4368259ff821 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"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
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">
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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diff changeset
626 <param name="selected_search_scheme" value="GridSearchCV"/>
1c4a241bef5c 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"/>
1c4a241bef5c 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">
1c4a241bef5c 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"/>
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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630 <repeat name="param_set">
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631 <param name="sp_list" value="[10, 50, 100, 300]"/>
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diff changeset
632 <param name="sp_name" value="n_estimators"/>
10
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diff changeset
633 </repeat>
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diff changeset
634 </section>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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635 </conditional>
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636 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
82b6104d4682 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" />
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
638 <param name="selected_column_selector_option" value="all_columns"/>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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639 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
640 <param name="header2" value="true" />
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
641 <param name="selected_column_selector_option2" value="all_columns"/>
82b6104d4682 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">
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
643 <param name="split_mode" value="nested_cv"/>
82b6104d4682 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">
82b6104d4682 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"/>
82b6104d4682 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"/>
82b6104d4682 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" />
82b6104d4682 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"/>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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649 </conditional>
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650 </conditional>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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651 <output name="outfile_result">
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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652 <assert_contents>
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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653 <has_n_columns n="4"/>
82b6104d4682 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" />
82b6104d4682 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>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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660 <![CDATA[
91bf3f0d7455 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
91bf3f0d7455 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`_.
91bf3f0d7455 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**
1c4a241bef5c 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
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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.
0
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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,
1c4a241bef5c 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))
0
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683
8
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684 - np_arange(0.01, 1, 0.1)
0
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685
8
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686 - np_random_choice(list(range(1, 51)) + [None], size=20)
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
687
8
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diff changeset
688 - scipy_stats_randin(1, 11)
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
689
8
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diff changeset
690 **Estimator / Preprocessor search (additional `:` in the front)**::
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
691
8
1c4a241bef5c 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
693
4368259ff821 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(),
4368259ff821 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()]
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
diff changeset
696
4368259ff821 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**::
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
698
4368259ff821 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)
4368259ff821 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)
10
82b6104d4682 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)
82b6104d4682 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')
82b6104d4682 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))
82b6104d4682 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)
82b6104d4682 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)
82b6104d4682 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>)
82b6104d4682 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>)
82b6104d4682 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>)
82b6104d4682 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>)
82b6104d4682 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>)
82b6104d4682 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>)
82b6104d4682 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)
82b6104d4682 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
4368259ff821 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
82b6104d4682 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
4368259ff821 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
82b6104d4682 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)
82b6104d4682 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
4368259ff821 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,
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
720 n_components=None, random_state=0, remove_zero_eig=False, tol=0)
10
82b6104d4682 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
4368259ff821 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,
4368259ff821 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
82b6104d4682 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
4368259ff821 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',
4368259ff821 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
82b6104d4682 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
728 n_iter=100, random_state=0, ridge_alpha=0.01, shuffle=True, verbose=False)
10
82b6104d4682 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
730 n_components=None, random_state=0, shuffle=False, solver='cd', tol=0.0001, verbose=0)
10
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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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)
82b6104d4682 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
733 n_components=None, random_state=0, ridge_alpha=0.01, tol=1e-08, verbose=False)
10
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
734 24 sklearn_decomposition.TruncatedSVD(algorithm='randomized', n_components=2, n_iter=5, random_state=0, tol=0.0)
82b6104d4682 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
736 kernel_params=None, n_components=100, random_state=0)
10
82b6104d4682 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)
82b6104d4682 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)
82b6104d4682 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)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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740 29 sklearn_cluster.FeatureAgglomeration(affinity='euclidean', compute_full_tree='auto', connectivity=None,
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
741 linkage='ward', memory=None, n_clusters=2, pooling_func=<function mean at 0x113078ae8>)
10
82b6104d4682 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)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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743 31 skrebate_SURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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744 32 skrebate_SURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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745 33 skrebate_MultiSURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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746 34 skrebate_MultiSURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
82b6104d4682 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
747 'sk_prep_all': All sklearn preprocessing estimators, i.e., 0-6
82b6104d4682 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
82b6104d4682 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
82b6104d4682 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
82b6104d4682 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
82b6104d4682 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
82b6104d4682 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
4368259ff821 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.
4368259ff821 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
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
756
4368259ff821 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.::
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
758
10
82b6104d4682 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
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
760
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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761
8
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
762
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff changeset
763 **Whether to do train_test_split?**
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
764
1c4a241bef5c 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`_
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
766
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
767
1c4a241bef5c 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
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
769 :height: 300
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
770 :width: 400
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
771
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
772
0
91bf3f0d7455 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
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
774 .. _`Scikit-learn model_selection RandomizedSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.RandomizedSearchCV.html
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
775 .. _`Tuning hyper-parameters`: http://scikit-learn.org/stable/modules/grid_search.html
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
776
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
777 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
91bf3f0d7455 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
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
779 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
780 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
diff changeset
781 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
782 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
783 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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784
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
785 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
786 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
787 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
788 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff changeset
789 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
790 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
8
1c4a241bef5c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
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
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
792
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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793 ]]>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
794 </help>
4
2e6540c11251 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 3
diff changeset
795 <expand macro="sklearn_citation">
2e6540c11251 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 3
diff changeset
796 <expand macro="skrebate_citation"/>
2e6540c11251 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 3
diff changeset
797 <expand macro="xgboost_citation"/>
7
4368259ff821 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
2e6540c11251 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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diff changeset
799 </expand>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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800 </tool>