Mercurial > repos > bgruening > sklearn_train_test_eval

annotate train_test_eval.xml @ 8:f2c240cce242 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 20:47:28 +0000
parents c9b521fcc3ac
children 0edcdeaad6f4
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f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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1 <tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@" profile="20.05">
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2 <description>fit a model using part of dataset and evaluate using the rest</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 <import>keras_macros.xml</import>
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6 </macros>
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7 <expand macro="python_requirements" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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8 <expand macro="macro_stdio" />
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 export HDF5_USE_FILE_LOCKING='FALSE';
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13 #if $input_options.selected_input == 'refseq_and_interval'
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14 bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' &&
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15 tabix -p bed '${target_file.element_identifier}.gz' &&
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16 #end if
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17 python '$__tool_directory__/train_test_eval.py'
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18 --inputs '$inputs'
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19 --estimator '$experiment_schemes.infile_estimator'
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20 #if $input_options.selected_input == 'seq_fasta'
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21 --fasta_path '$input_options.fasta_path'
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22 #elif $input_options.selected_input == 'refseq_and_interval'
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23 --ref_seq '$input_options.ref_genome_file'
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24 --interval '$input_options.interval_file'
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25 --targets "`pwd`/${target_file.element_identifier}.gz"
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26 #else
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27 --infile1 '$input_options.infile1'
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28 #end if
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29 --infile2 '$input_options.infile2'
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30 --outfile_result "`pwd`/tmp_outfile_result"
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31 #if $save != 'nope'
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32 --outfile_object '$outfile_object'
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33 #end if
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34 #if $save == 'save_weights'
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35 --outfile_weights '$outfile_weights'
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36 #end if
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37 #if $experiment_schemes.test_split.split_algos.shuffle == 'group'
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38 --groups '$experiment_schemes.test_split.split_algos.groups_selector.infile_g'
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39 #end if
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40 >'$outfile_result' && cp tmp_outfile_result '$outfile_result';
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41
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42 ]]>
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43 </command>
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44 <configfiles>
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45 <inputs name="inputs" />
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46 </configfiles>
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47 <inputs>
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48 <conditional name="experiment_schemes">
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49 <param name="selected_exp_scheme" type="select" label="Select a scheme">
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50 <option value="train_test" selected="true">Train and Test</option>
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51 <option value="train_val_test">Train, Validate and Test</option>
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52 </param>
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53 <when value="train_test">
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54 <expand macro="estimator_and_hyperparameter" />
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55 <section name="test_split" title="Test holdout" expanded="false">
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56 <expand macro="train_test_split_params">
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57 <expand macro="cv_groups" />
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58 </expand>
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59 </section>
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60 <section name="metrics" title="Metrics for evaluation" expanded="false">
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61 <expand macro="scoring_selection" />
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62 </section>
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63 </when>
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64 <when value="train_val_test">
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65 <expand macro="estimator_and_hyperparameter" />
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66 <section name="test_split" title="Test holdout" expanded="false">
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67 <expand macro="train_test_split_params">
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68 <expand macro="cv_groups" />
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69 </expand>
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70 </section>
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71 <section name="val_split" title="Validation holdout (recommend using the same method for both validation and test)" expanded="false">
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72 <expand macro="train_test_split_params" />
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73 </section>
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74 <section name="metrics" title="Metrics for evaluation" expanded="false">
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75 <expand macro="scoring_selection" />
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76 </section>
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77 </when>
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78 </conditional>
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79 <expand macro="sl_mixed_input_plus_sequence" />
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80 <param name="save" type="select" label="Save the fitted model" help="For security reason, deep learning models will be saved into two datasets, model skeleton and weights.">
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81 <option value="nope" selected="true">Nope, save is unnecessary</option>
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82 <option value="save_estimator">Fitted whole estimator (excluding deep learning)</option>
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83 <option value="save_weights">Model skeleton and weights, for deep learning exclusively</option>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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84 </param>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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85 </inputs>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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86 <outputs>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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87 <data format="tabular" name="outfile_result" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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88 <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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89 <filter>save != 'nope'</filter>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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90 </data>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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91 <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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92 <filter>save == 'save_weights'</filter>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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93 </data>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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94 </outputs>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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95 <tests>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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96 <test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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97 <conditional name="experiment_schemes">
8
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98 <param name="selected_exp_scheme" value="train_val_test" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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99 <param name="infile_estimator" value="keras_model04" ftype="zip" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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100 <section name="hyperparams_swapping">
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101 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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102 <repeat name="param_set">
8
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103 <param name="sp_value" value="999" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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104 <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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105 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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106 <repeat name="param_set">
8
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107 <param name="sp_value" value="999" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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108 <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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109 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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110 <repeat name="param_set">
8
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111 <param name="sp_value" value="0.1" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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112 <param name="sp_name" value="lr" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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113 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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114 <repeat name="param_set">
8
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115 <param name="sp_value" value="'adamax'" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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116 <param name="sp_name" value="optimizer" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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117 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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118 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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119 <section name="test_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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120 <conditional name="split_algos">
8
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121 <param name="shuffle" value="simple" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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122 <param name="test_size" value="0.2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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123 <param name="random_state" value="123" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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124 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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125 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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126 <section name="val_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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127 <conditional name="split_algos">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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128 <param name="shuffle" value="simple" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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129 <param name="test_size" value="0.2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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130 <param name="random_state" value="456" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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131 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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132 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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133 <section name="metrics">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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134 <conditional name="scoring">
8
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135 <param name="primary_scoring" value="r2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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136 <param name="secondary_scoring" value="neg_mean_absolute_error" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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137 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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138 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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139 </conditional>
8
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140 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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141 <param name="header1" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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142 <param name="selected_column_selector_option" value="all_columns" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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143 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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144 <param name="header2" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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145 <param name="selected_column_selector_option2" value="all_columns" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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146 <param name="save" value="save_weights" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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147 <output name="outfile_result">
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148 <assert_contents>
8
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149 <has_n_columns n="2" />
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150 <has_text text="0.6384" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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151 <has_text text="-6.072" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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152 </assert_contents>
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153 </output>
8
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154 <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="5" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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155 <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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156 </test>
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157 <test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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158 <conditional name="experiment_schemes">
8
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159 <param name="selected_exp_scheme" value="train_val_test" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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160 <param name="infile_estimator" value="keras_model04" ftype="zip" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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161 <section name="hyperparams_swapping">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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162 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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163 <repeat name="param_set">
8
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164 <param name="sp_value" value="999" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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165 <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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166 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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167 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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168 <param name="sp_value" value="999" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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169 <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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170 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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171 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
172 <param name="sp_value" value="0.1" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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173 <param name="sp_name" value="lr" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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174 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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175 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
176 <param name="sp_value" value="'adamax'" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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177 <param name="sp_name" value="optimizer" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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178 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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179 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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180 <section name="test_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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181 <conditional name="split_algos">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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182 <param name="shuffle" value="group" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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183 <param name="group_names" value="test" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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184 <section name="groups_selector">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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185 <param name="infile_g" value="regression_groups.tabular" ftype="tabular" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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186 <param name="header_g" value="true" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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187 <conditional name="column_selector_options_g">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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188 <param name="selected_column_selector_option_g" value="by_index_number" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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189 <param name="col_g" value="1" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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190 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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191 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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192 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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193 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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194 <section name="val_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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195 <conditional name="split_algos">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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196 <param name="shuffle" value="group" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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197 <param name="group_names" value="validation" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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198 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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199 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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200 <section name="metrics">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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201 <conditional name="scoring">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
202 <param name="primary_scoring" value="r2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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203 <param name="secondary_scoring" value="neg_mean_absolute_error" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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204 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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205 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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206 </conditional>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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207 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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208 <param name="header1" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
209 <param name="selected_column_selector_option" value="all_columns" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
210 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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211 <param name="header2" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
212 <param name="selected_column_selector_option2" value="all_columns" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
213 <param name="save" value="save_weights" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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214 <output name="outfile_result">
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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215 <assert_contents>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
216 <has_n_columns n="2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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217 <has_text text="0.627" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
218 <has_text text="-6.012" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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219 </assert_contents>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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220 </output>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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221 <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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222 </test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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223 <test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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224 <conditional name="experiment_schemes">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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225 <param name="selected_exp_scheme" value="train_test" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
226 <param name="infile_estimator" value="pipeline10" ftype="zip" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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227 <section name="hyperparams_swapping">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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228 <param name="infile_params" value="get_params10.tabular" ftype="tabular" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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229 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
230 <param name="sp_value" value="10" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
231 <param name="sp_name" value="adaboostregressor__random_state" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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232 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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233 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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234 <param name="sp_value" value=": sklearn_tree.ExtraTreeRegressor(random_state=0)" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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235 <param name="sp_name" value="adaboostregressor__base_estimator" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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236 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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237 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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238 <section name="test_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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239 <conditional name="split_algos">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
240 <param name="shuffle" value="simple" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
241 <param name="test_size" value="0.2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
242 <param name="random_state" value="123" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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243 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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244 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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245 <section name="val_split">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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246 <conditional name="split_algos">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
247 <param name="shuffle" value="simple" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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248 <param name="test_size" value="0.2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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249 <param name="random_state" value="456" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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250 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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251 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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252 <section name="metrics">
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253 <conditional name="scoring">
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254 <param name="primary_scoring" value="r2" />
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255 <param name="secondary_scoring" value="neg_mean_absolute_error" />
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256 </conditional>
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257 </section>
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258 </conditional>
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259 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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260 <param name="header1" value="true" />
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261 <param name="selected_column_selector_option" value="all_columns" />
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262 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
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263 <param name="header2" value="true" />
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264 <param name="selected_column_selector_option2" value="all_columns" />
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265 <param name="save" value="nope" />
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266 <output name="outfile_result" file="train_test_eval03.tabular" />
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267 </test>
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268 </tests>
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269 <help>
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270 <![CDATA[
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271 **What it does**
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272
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273 Given an estimator and dataset, this tool fits the estimator with part of the datasets and evalue the performance of the fitted estimator on the rest of the datasets. It consists of two modes: train-test and train-val-test.
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274
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275 - train-test: data sets will be split into train and test portions. Estimator is training on the train portion, and performance is evaluated on the test portion.
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276
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277 - train-val-test: data sets are split into three portions, train, val and test. Validations happen along with the training process, which is often useful in **deep learnings**.
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278
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279 **Output**
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280
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281 Performance scores.
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282
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283 ]]>
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284 </help>
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285 <expand macro="sklearn_citation">
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286 <expand macro="skrebate_citation" />
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287 <expand macro="xgboost_citation" />
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288 <expand macro="keras_citation" />
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289 </expand>
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290 </tool>