Mercurial > repos > bgruening > sklearn_searchcv

annotate search_model_validation.xml @ 7:4368259ff821 draft

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author bgruening
date Sun, 30 Dec 2018 01:51:27 -0500
parents 7509d7059040
children 1c4a241bef5c
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1 <tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@">
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2 <description>using exhausitive or randomized search</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements">
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7 <requirement type="package" version="0.6">skrebate</requirement>
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8 <requirement type="package" version="0.4.2">imbalanced-learn</requirement>
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9 </expand>
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10 <expand macro="macro_stdio"/>
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11 <version_command>echo "@VERSION@"</version_command>
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12 <command>
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13 <![CDATA[
7
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14 python '$__tool_directory__/search_model_validation.py'
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15 '$inputs'
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16 '$search_schemes.infile_pipeline'
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17 '$input_options.infile1'
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18 '$input_options.infile2'
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19 '$outfile_result'
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20 #if $save:
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21 '$outfile_estimator'
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22 #end if
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23 ]]>
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24 </command>
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25 <configfiles>
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26 <inputs name="inputs" />
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27 </configfiles>
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28 <inputs>
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29 <conditional name="search_schemes">
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30 <param name="selected_search_scheme" type="select" label="Select a model selection search scheme:">
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31 <option value="GridSearchCV" selected="true">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option>
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32 <option value="RandomizedSearchCV">RandomizedSearchCV - Randomized search on hyper parameters for an estimator</option>
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33 </param>
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34 <when value="GridSearchCV">
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35 <expand macro="search_cv_estimator"/>
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36 <section name="options" title="Advanced Options for SearchCV" expanded="false">
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37 <expand macro="search_cv_options"/>
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38 </section>
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39 </when>
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40 <when value="RandomizedSearchCV">
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41 <expand macro="search_cv_estimator"/>
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42 <section name="options" title="Advanced Options for SearchCV" expanded="false">
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43 <expand macro="search_cv_options"/>
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44 <param argument="n_iter" type="integer" value="10" label="Number of parameter settings that are sampled"/>
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45 <expand macro="random_state"/>
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46 </section>
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47 </when>
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48 </conditional>
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49 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Save the best estimator/pipeline?"/>
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50 <expand macro="sl_mixed_input"/>
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51 </inputs>
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52 <outputs>
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53 <data format="tabular" name="outfile_result"/>
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54 <data format="zip" name="outfile_estimator" label="${tool.name}: best estimator on ${on_string}">
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55 <filter>save</filter>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="selected_search_scheme" value="GridSearchCV"/>
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61 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
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62 <conditional name="search_param_selector">
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63 <param name="search_p" value="C: [1, 10, 100, 1000]"/>
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64 <param name="selected_param_type" value="final_estimator_p"/>
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65 </conditional>
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66 <conditional name="search_param_selector">
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67 <param name="search_p" value="k: [-1, 3, 5, 7, 9]"/>
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68 <param name="selected_param_type" value="prep_2_p"/>
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69 </conditional>
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70 <param name="error_score" value="false"/>
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71 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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72 <param name="header1" value="true" />
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73 <param name="selected_column_selector_option" value="all_columns"/>
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74 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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75 <param name="header2" value="true" />
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76 <param name="selected_column_selector_option2" value="all_columns"/>
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77 <output name="outfile_result">
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78 <assert_contents>
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79 <has_n_columns n="13"/>
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80 <has_text text="0.7938837807353147"/>
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81 <has_text text="{'estimator__C': 1, 'preprocessing_2__k': 9}"/>
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82 </assert_contents>
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83 </output>
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84 </test>
5
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85 <test expect_failure="true">
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86 <param name="selected_search_scheme" value="GridSearchCV"/>
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87 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
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88 <conditional name="search_param_selector">
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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89 <param name="search_p" value="C: [1, 10, 100, 1000]"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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90 <param name="selected_param_type" value="final_estimator_p"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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91 </conditional>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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92 <conditional name="search_param_selector">
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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diff changeset
93 <param name="search_p" value="k: [-1, 3, 5, 7, 9]"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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94 <param name="selected_param_type" value="prep_2_p"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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95 </conditional>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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96 <param name="error_score" value="true"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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97 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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98 <param name="header1" value="true" />
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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99 <param name="selected_column_selector_option" value="all_columns"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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100 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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101 <param name="header2" value="true" />
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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102 <param name="selected_column_selector_option2" value="all_columns"/>
0987bc3904a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
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103 </test>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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104 <test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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105 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
4
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106 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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107 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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108 <param name="search_p" value="C: [1, 10, 100, 1000]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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109 <param name="selected_param_type" value="final_estimator_p"/>
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110 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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111 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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112 <param name="search_p" value="kernel: ['linear', 'poly', 'rbf', 'sigmoid']"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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113 <param name="selected_param_type" value="final_estimator_p"/>
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114 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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115 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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116 <param name="search_p" value="k: [3, 5, 7, 9]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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117 <param name="selected_param_type" value="prep_2_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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118 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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119 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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120 <param name="search_p" value="with_centering: [True, False]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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121 <param name="selected_param_type" value="prep_1_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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122 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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123 <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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124 <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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125 <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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126 <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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127 <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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128 <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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129 <output name="outfile_result" >
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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130 <assert_contents>
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131 <has_n_columns n="15" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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132 <has_text text="param_preprocessing_1__with_centering"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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133 </assert_contents>
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134 </output>
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135 </test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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136 <test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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137 <param name="selected_search_scheme" value="RandomizedSearchCV"/>
4
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diff changeset
138 <param name="infile_pipeline" value="pipeline03" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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139 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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140 <param name="search_p" value="n_estimators: np_arange(50, 1001, 50)"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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141 <param name="selected_param_type" value="final_estimator_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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142 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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143 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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144 <param name="search_p" value="max_depth: scipy_stats_randint(1, 51)"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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145 <param name="selected_param_type" value="final_estimator_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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146 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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147 <conditional name="search_param_selector">
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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148 <param name="search_p" value="gamma: scipy_stats_uniform(0., 1.)"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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149 <param name="selected_param_type" value="final_estimator_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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150 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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151 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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152 <param name="search_p" value="random_state: [324089]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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153 <param name="selected_param_type" value="final_estimator_p"/>
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154 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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155 <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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156 <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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157 <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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158 <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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159 <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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160 <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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161 <output name="outfile_result" >
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162 <assert_contents>
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163 <has_n_columns n="15" />
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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164 <has_text text="param_estimator__max_depth"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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165 </assert_contents>
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166 </output>
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167 </test>
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168 <test>
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169 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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170 <param name="infile_pipeline" value="pipeline04" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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171 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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172 <param name="search_p" value="random_state: list(range(100, 1001, 100))"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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173 <param name="selected_param_type" value="final_estimator_p"/>
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174 </conditional>
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175 <conditional name="search_param_selector">
7
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176 <param name="search_p" value="estimator-: [sklearn_ensemble.ExtraTreesClassifier(n_estimators=100, random_state=324089)]"/>
0
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177 <param name="selected_param_type" value="prep_1_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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178 </conditional>
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179 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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180 <param name="header1" value="true" />
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181 <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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182 <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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183 <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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184 <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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185 <output name="outfile_result">
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186 <assert_contents>
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187 <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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188 <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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189 </assert_contents>
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190 </output>
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191 </test>
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192 <test>
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193 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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194 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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195 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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196 <param name="search_p" value="C: [1, 10, 100, 1000]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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197 <param name="selected_param_type" value="final_estimator_p"/>
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198 </conditional>
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199 <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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200 <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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201 <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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202 <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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203 <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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204 <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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205 <output name="outfile_estimator" file="searchCV01" compare="sim_size" delta="1"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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206 </test>
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207 <test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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208 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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diff changeset
209 <param name="infile_pipeline" value="pipeline06" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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210 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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211 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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212 <param name="selected_param_type" value="final_estimator_p"/>
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213 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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214 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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215 <param name="search_p" value="random_state: [324089]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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216 <param name="selected_param_type" value="final_estimator_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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217 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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218 <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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219 <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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220 <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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221 <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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222 <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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223 <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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224 <output name="outfile_result">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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225 <assert_contents>
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226 <has_n_columns n="13"/>
7
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diff changeset
227 <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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228 </assert_contents>
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229 </output>
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230 </test>
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231 <test>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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232 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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diff changeset
233 <param name="infile_pipeline" value="pipeline07" ftype="zip"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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234 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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235 <param name="search_p" value="n_estimators: [10, 50, 100, 200]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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236 <param name="selected_param_type" value="final_estimator_p"/>
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237 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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238 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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239 <param name="search_p" value="random_state: [324089]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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240 <param name="selected_param_type" value="final_estimator_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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241 </conditional>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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242 <conditional name="search_param_selector">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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243 <param name="search_p" value="gamma: [1.0, 2.0]"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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244 <param name="selected_param_type" value="prep_1_p"/>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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245 </conditional>
7
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diff changeset
246 <param name='selected_cv' value="default"/>
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diff changeset
247 <param name="n_splits" value="3"/>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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248 <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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249 <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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250 <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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251 <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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252 <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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253 <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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254 <output name="outfile_result">
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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255 <assert_contents>
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256 <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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257 <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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258 </assert_contents>
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259 </output>
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260 </test>
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261 <test>
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262 <param name="selected_search_scheme" value="GridSearchCV"/>
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263 <param name="infile_pipeline" value="pipeline08" ftype="zip"/>
0
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264 <conditional name="search_param_selector">
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265 <param name="search_p" value="n_estimators: [10, 50, 100, 200]"/>
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266 <param name="selected_param_type" value="final_estimator_p"/>
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267 </conditional>
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268 <conditional name="search_param_selector">
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269 <param name="search_p" value="random_state: [324089]"/>
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270 <param name="selected_param_type" value="final_estimator_p"/>
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271 </conditional>
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272 <conditional name="search_param_selector">
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273 <param name="search_p" value="linkage: ['ward', 'complete', 'average']"/>
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274 <param name="selected_param_type" value="prep_1_p"/>
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275 </conditional>
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276 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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277 <param name="header1" value="true" />
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278 <param name="selected_column_selector_option" value="all_columns"/>
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279 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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280 <param name="header2" value="true" />
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281 <param name="selected_column_selector_option2" value="all_columns"/>
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282 <output name="outfile_result">
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283 <assert_contents>
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284 <has_text_matching expression=".+0.08045977011494253[^/w]+10[^/w]" />
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285 </assert_contents>
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286 </output>
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287 </test>
2
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288 <test>
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289 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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290 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
2
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291 <conditional name="search_param_selector">
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292 <param name="search_p" value="C: [1, 10, 100, 1000]"/>
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293 <param name="selected_param_type" value="final_estimator_p"/>
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294 </conditional>
7
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295 <param name='selected_cv' value="StratifiedKFold"/>
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296 <param name="n_splits" value="3"/>
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297 <param name="shuffle" value="true" />
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298 <param name="random_state" value="10"/>
2
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299 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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300 <param name="header1" value="true" />
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301 <param name="selected_column_selector_option" value="all_columns"/>
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302 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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303 <param name="header2" value="true" />
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304 <param name="selected_column_selector_option2" value="all_columns"/>
5
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305 <output name="outfile_estimator" file="searchCV02" compare="sim_size" delta="1"/>
2
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306 </test>
3
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307 <test>
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308 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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309 <param name="infile_pipeline" value="pipeline03" ftype="zip"/>
3
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310 <conditional name="search_param_selector">
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311 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/>
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312 <param name="selected_param_type" value="final_estimator_p"/>
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313 </conditional>
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314 <conditional name="search_param_selector">
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315 <param name="search_p" value="random_state: [324089]"/>
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316 <param name="selected_param_type" value="final_estimator_p"/>
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317 </conditional>
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318 <param name="primary_scoring" value="balanced_accuracy"/>
7
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319 <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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320 <param name="n_splits" value="3"/>
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321 <param name="shuffle" value="true" />
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322 <param name="random_state" value="10"/>
3
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323 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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324 <param name="header1" value="true" />
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325 <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
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326 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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327 <param name="header2" value="true" />
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328 <param name="selected_column_selector_option2" value="all_columns"/>
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329 <output name="outfile_result" >
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330 <assert_contents>
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331 <has_n_columns n="13" />
5
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332 <has_text text="0.09003449195911103"/>
3
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333 </assert_contents>
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334 </output>
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335 </test>
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336 <test>
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337 <param name="selected_search_scheme" value="GridSearchCV"/>
4
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338 <param name="infile_pipeline" value="pipeline09" ftype="zip"/>
3
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339 <conditional name="search_param_selector">
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340 <param name="search_p" value="n_neighbors: [50, 100, 150, 200]"/>
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341 <param name="selected_param_type" value="prep_1_p"/>
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342 </conditional>
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343 <conditional name="search_param_selector">
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344 <param name="search_p" value="random_state: [324089]"/>
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345 <param name="selected_param_type" value="final_estimator_p"/>
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346 </conditional>
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347 <param name="primary_scoring" value="explained_variance"/>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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348 <param name="secondary_scoring" value="neg_mean_squared_error,r2"/>
7
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349 <param name='selected_cv' value="StratifiedKFold"/>
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350 <param name="n_splits" value="3"/>
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351 <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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352 <param name="random_state" value="10"/>
3
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353 <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
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354 <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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355 <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
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356 <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
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357 <param name="header2" value="true" />
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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358 <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
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359 <output name="outfile_result" >
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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360 <assert_contents>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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361 <has_n_columns n="25" />
7
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362 <has_text text="0.7879267424165166"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 6
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363 <has_text text="0.787865425577799"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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364 <has_text text="-29.40436189868029"/>
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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365 </assert_contents>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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366 </output>
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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367 </test>
6
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368 <test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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369 <param name="selected_search_scheme" value="GridSearchCV"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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370 <param name="infile_pipeline" value="pipeline02" ftype="zip"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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371 <conditional name="search_param_selector">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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372 <param name="search_p" value="eps: [0.01, 0.001]"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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373 <param name="selected_param_type" value="final_estimator_p"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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374 </conditional>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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375 <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
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376 <param name="header1" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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377 <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
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378 <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
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379 <param name="header2" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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380 <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
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381 <output name="outfile_result">
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382 <assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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383 <has_n_columns n="12"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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384 <has_text text="0.7762968161366681" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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385 </assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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386 </output>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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387 </test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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388 <test>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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389 <param name="selected_search_scheme" value="GridSearchCV"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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390 <param name="infile_pipeline" value="pipeline05" ftype="zip"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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391 <conditional name="search_param_selector">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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392 <param name="search_p" value="n_estimators: [10, 50, 100, 300]"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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393 <param name="selected_param_type" value="final_estimator_p"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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394 </conditional>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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395 <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
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396 <param name="header1" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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397 <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
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398 <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
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399 <param name="header2" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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400 <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
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401 <output name="outfile_result">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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402 <assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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403 <has_n_columns n="12"/>
7
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diff changeset
404 <has_text text="0.8176576686816003" />
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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405 </assert_contents>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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406 </output>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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407 </test>
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408 <test expect_failure="true">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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409 <param name="selected_search_scheme" value="GridSearchCV"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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410 <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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411 <conditional name="search_param_selector">
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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412 <param name="search_p" value="C: open('~/.ssh/authorized_keys', 'r').read()"/>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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413 <param name="selected_param_type" value="final_estimator_p"/>
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414 </conditional>
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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415 <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
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416 <param name="header1" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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417 <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
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418 <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
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419 <param name="header2" value="true" />
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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420 <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
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421 </test>
7
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422 <test>
6
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423 <param name="selected_search_scheme" value="GridSearchCV"/>
7
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424 <param name="infile_pipeline" value="pipeline10" ftype="zip"/>
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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425 <conditional name="search_param_selector">
7
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426 <param name="search_p" value="base_estimator-: [sklearn_tree.DecisionTreeRegressor(random_state=0), sklearn_tree.ExtraTreeRegressor(random_state=0)]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
427 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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428 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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429 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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430 <param name="search_p" value="random_state: [10]"/>
6
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431 <param name="selected_param_type" value="final_estimator_p"/>
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432 </conditional>
7
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433 <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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434 <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
435 <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
436 <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
437 <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
438 <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
439 <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
440 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
441 <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
442 <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
443 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
444 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
445 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
446 <test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
447 <param name="selected_search_scheme" value="GridSearchCV"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
448 <param name="infile_pipeline" value="pipeline09" ftype="zip"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
449 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
450 <param name="search_p" value=": [sklearn_feature_selection.SelectKBest(),
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
451 sklearn_feature_selection.VarianceThreshold(), skrebate_ReliefF(), sklearn_preprocessing.RobustScaler()]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
452 <param name="selected_param_type" value="prep_1_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
453 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
454 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
455 <param name="search_p" value="random_state: [10]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
456 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
457 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 <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
465 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
466 <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
467 <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
468 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
469 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
470 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
471 <test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
472 <param name="selected_search_scheme" value="GridSearchCV"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
473 <param name="infile_pipeline" value="pipeline09" ftype="zip"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
474 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
475 <param name="search_p" value=": [None,'sk_prep_all', 8, 14, skrebate_ReliefF(n_features_to_select=12)]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
476 <param name="selected_param_type" value="prep_1_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
477 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
478 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
479 <param name="search_p" value="random_state: [10]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
480 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
481 </conditional>
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 5
diff changeset
482 <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
483 <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
484 <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
485 <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
486 <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
487 <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
488 <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
489 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
490 <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
491 <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
492 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
493 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
494 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
495 <test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
496 <param name="selected_search_scheme" value="GridSearchCV"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
497 <param name="infile_pipeline" value="pipeline11" ftype="zip"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
498 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
499 <param name="search_p" value="n_neighbors: [3,4,5]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
500 <param name="selected_param_type" value="prep_1_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
501 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
502 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
503 <param name="search_p" value="random_state: [10]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
504 <param name="selected_param_type" value="prep_1_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
505 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
506 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
507 <param name="search_p" value="n_estimators:[10, 50, 100, 500]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
508 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
509 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
510 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
511 <param name="search_p" value="random_state: [10]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
512 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 6
diff changeset
513 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
514 <param name="primary_scoring" value="f1_macro"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
515 <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
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diff changeset
516 <param name="n_splits" value="5"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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diff changeset
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
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diff changeset
523 <output name="outfile_result">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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524 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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525 <has_n_columns n="33"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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526 <has_text text="0.9945648481554453"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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527 <has_text text="0.9988888888888889"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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528 <has_text text="0.998"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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529 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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530 </output>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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531 </test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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532 <test>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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533 <param name="selected_search_scheme" value="GridSearchCV"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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534 <param name="infile_pipeline" value="pipeline12" ftype="zip"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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535 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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536 <param name="search_p" value="estimator__n_estimators: [10, 100, 200]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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537 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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538 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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539 <conditional name="search_param_selector">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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540 <param name="search_p" value="n_features_to_select: [10, None]"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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541 <param name="selected_param_type" value="final_estimator_p"/>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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542 </conditional>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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543 <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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544 <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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545 <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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546 <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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547 <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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548 <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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549 <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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550 <output name="outfile_result">
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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551 <assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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552 <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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553 <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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554 </assert_contents>
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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555 </output>
6
7509d7059040 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
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556 </test>
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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557 </tests>
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558 <help>
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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559 <![CDATA[
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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560 **What it does**
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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561 Searches optimized parameter values for an estimator or pipeline through either exhaustive grid cross validation search or Randomized cross validation search.
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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562 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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563
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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564 **How to choose search patameters?**
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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565
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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566 Please refer to `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and `xgboost`_ for estimator parameters.
3
f9fea8323bcb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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567 Refer to `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_ and `skrebate`_ for parameter in the pre-processing steps.
0
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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568
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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569 **Search parameter input** accepts parameter and setting in key:value pair. One pair per input box. Setting can be list, numpy array, or distribution.
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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570 The evaluation of settings supports operations in Math, 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.
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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571
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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572 **Examples:**
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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573
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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574 - K: [3, 5, 7, 9]
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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575
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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576 - n_estimators: list(range(50, 1001, 50))
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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577
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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578 - gamma: np_arange(0.01, 1, 0.1)
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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579
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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580 - alpha: np_random_choice(list(range(1, 51)) + [None], size=20)
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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581
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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582 - max_depth: scipy_stats_randin(1, 11)
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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583
7
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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584 **Estimator search/eval (additional '-')**::
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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585
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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586 base_estimator-: [sklearn_tree.DecisionTreeRegressor(), sklearn_tree.ExtraTreeRegressor()]
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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587
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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588 **Preprocessors search/swap**::
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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589
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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590 : [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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591 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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592
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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593 **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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594
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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595 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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596 1 sklearn_preprocessing.Binarizer(copy=True, threshold=0.0)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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597 2 sklearn_preprocessing.Imputer(axis=0, copy=True, missing_values='NaN', strategy='mean', verbose=0)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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598 3 sklearn_preprocessing.MaxAbsScaler(copy=True)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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599 4 sklearn_preprocessing.Normalizer(copy=True, norm='l2')
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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600 5 sklearn_preprocessing.MinMaxScaler(copy=True, feature_range=(0, 1))
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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601 6 sklearn_preprocessing.PolynomialFeatures(degree=2, include_bias=True, interaction_only=False)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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602 7 sklearn_preprocessing.RobustScaler(copy=True, quantile_range=(25.0, 75.0), with_centering=True, with_scaling=True)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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603 8 sklearn_feature_selection.SelectKBest(k=10, score_func=<function f_classif at 0x113806d90>)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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604 9 sklearn_feature_selection.GenericUnivariateSelect(mode='percentile', param=1e-05, score_func=<function f_classif at 0x113806d90>)
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605 10 sklearn_feature_selection.SelectPercentile(percentile=10, score_func=<function f_classif at 0x113806d90>)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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606 11 sklearn_feature_selection.SelectFpr(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
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607 12 sklearn_feature_selection.SelectFdr(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
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608 13 sklearn_feature_selection.SelectFwe(alpha=0.05, score_func=<function f_classif at 0x113806d90>)
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609 14 sklearn_feature_selection.VarianceThreshold(threshold=0.0)
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610 15 sklearn_decomposition.FactorAnalysis(copy=True, iterated_power=3, max_iter=1000, n_components=None,
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611 noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01)
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612 16 sklearn_decomposition.FastICA(algorithm='parallel', fun='logcosh', fun_args=None,
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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613 max_iter=200, n_components=None, random_state=0, tol=0.0001, w_init=None, whiten=True)
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614 17 sklearn_decomposition.IncrementalPCA(batch_size=None, copy=True, n_components=None, whiten=False)
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615 18 sklearn_decomposition.KernelPCA(alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto',
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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616 fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None,
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617 n_components=None, random_state=0, remove_zero_eig=False, tol=0)
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618 19 sklearn_decomposition.LatentDirichletAllocation(batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7,
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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619 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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620 n_topics=None, perp_tol=0.1, random_state=0, topic_word_prior=None, total_samples=1000000.0, verbose=0)
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621 20 sklearn_decomposition.MiniBatchDictionaryLearning(alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars',
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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622 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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623 transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False)
4368259ff821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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624 21 sklearn_decomposition.MiniBatchSparsePCA(alpha=1, batch_size=3, callback=None, method='lars', n_components=None,
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625 n_iter=100, random_state=0, ridge_alpha=0.01, shuffle=True, verbose=False)
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626 22 sklearn_decomposition.NMF(alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200,
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627 n_components=None, random_state=0, shuffle=False, solver='cd', tol=0.0001, verbose=0)
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628 23 sklearn_decomposition.PCA(copy=True, iterated_power='auto', n_components=None, random_state=0, svd_solver='auto', tol=0.0, whiten=False)
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629 24 sklearn_decomposition.SparsePCA(U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars',
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630 n_components=None, random_state=0, ridge_alpha=0.01, tol=1e-08, verbose=False)
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631 25 sklearn_decomposition.TruncatedSVD(algorithm='randomized', n_components=2, n_iter=5, random_state=0, tol=0.0)
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632 26 sklearn_kernel_approximation.Nystroem(coef0=None, degree=None, gamma=None, kernel='rbf',
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633 kernel_params=None, n_components=100, random_state=0)
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634 27 sklearn_kernel_approximation.RBFSampler(gamma=1.0, n_components=100, random_state=0)
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635 28 sklearn_kernel_approximation.AdditiveChi2Sampler(sample_interval=None, sample_steps=2)
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636 29 sklearn_kernel_approximation.SkewedChi2Sampler(n_components=100, random_state=0, skewedness=1.0)
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637 30 sklearn_cluster.FeatureAgglomeration(affinity='euclidean', compute_full_tree='auto', connectivity=None,
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638 linkage='ward', memory=None, n_clusters=2, pooling_func=<function mean at 0x113078ae8>)
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639 31 skrebate_ReliefF(discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False)
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640 32 skrebate_SURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
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641 33 skrebate_SURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
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642 34 skrebate_MultiSURF(discrete_threshold=10, n_features_to_select=10, verbose=False)
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643 35 skrebate_MultiSURFstar(discrete_threshold=10, n_features_to_select=10, verbose=False)
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644 'sk_prep_all': All sklearn preprocessing estimators, i.e., 0-7
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645 'fs_all': All feature_selection estimators, i.e., 8-14
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646 'decomp_all': All decomposition estimators, i.e., 15-25
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647 'k_appr_all': All kernel_approximation estimators, i.e., 26-29
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648 'reb_all': All skrebate estimators, i.e., 31-35
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649 'all_0': All except the imbalanced-learn samplers, i.e., 0-35
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650 'imb_all': All imbalanced-learn sampling methods, i.e., 36-54.
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651 **CAUTION**: Mix of imblearn and other preprocessors may not work.
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652 None: opt out of preprocessor
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653
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654 Support mix (CAUTION: Mix of imblearn and other preprocessors may not work), e.g.::
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655
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656 : [None, 'sk_prep_all', 22, 'k_appr_all', sklearn_feature_selection.SelectKBest(k=50)]
0
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657
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658
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659 .. _`Scikit-learn model_selection GridSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html
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660 .. _`Scikit-learn model_selection RandomizedSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.RandomizedSearchCV.html
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661 .. _`Tuning hyper-parameters`: http://scikit-learn.org/stable/modules/grid_search.html
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662
91bf3f0d7455 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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663 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm
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664 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model
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665 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble
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666 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes
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667 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree
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668 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors
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669 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html
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670
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671 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing
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672 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection
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673 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition
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674 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation
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675 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html
3
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676 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/
0
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677
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678 ]]>
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679 </help>
4
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680 <expand macro="sklearn_citation">
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681 <expand macro="skrebate_citation"/>
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682 <expand macro="xgboost_citation"/>
7
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683 <expand macro="imblearn_citation"/>
4
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684 </expand>
0
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685 </tool>