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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author bgruening
date Mon, 02 Oct 2023 09:12:23 +0000
parents f2c240cce242
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0edcdeaad6f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
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1 <tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@" profile="@PROFILE@">
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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>
8
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7 <expand macro="python_requirements" />
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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>
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85 </inputs>
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86 <outputs>
8
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87 <data format="tabular" name="outfile_result" />
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88 <data format="h5mlm" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
0
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" />
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99 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
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">
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103 <param name="sp_value" value="999" />
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104 <param name="sp_name" value="layers_1_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" />
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108 <param name="sp_name" value="layers_3_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">
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111 <param name="sp_value" value="0.1" />
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112 <param name="sp_name" value="learning_rate" />
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
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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" />
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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">
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135 <param name="primary_scoring" value="r2" />
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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
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142 <param name="selected_column_selector_option" value="all_columns" />
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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" />
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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" />
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147 <output name="outfile_result">
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148 <assert_contents>
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149 <has_n_columns n="2" />
0
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150 </assert_contents>
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151 </output>
8
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152 <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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153 </test>
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154 <test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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155 <conditional name="experiment_schemes">
8
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156 <param name="selected_exp_scheme" value="train_val_test" />
14
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157 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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158 <section name="hyperparams_swapping">
8
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159 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" />
0
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160 <repeat name="param_set">
8
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161 <param name="sp_value" value="999" />
14
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162 <param name="sp_name" value="layers_1_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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163 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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164 <repeat name="param_set">
8
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165 <param name="sp_value" value="999" />
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166 <param name="sp_name" value="layers_3_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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167 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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168 <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
169 <param name="sp_value" value="0.1" />
14
0edcdeaad6f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
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diff changeset
170 <param name="sp_name" value="learning_rate" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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171 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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172 <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
173 <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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diff changeset
174 <param name="sp_name" value="optimizer" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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175 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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176 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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diff changeset
177 <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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diff changeset
178 <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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diff changeset
179 <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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diff changeset
180 <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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181 <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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182 <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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183 <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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184 <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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diff changeset
185 <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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186 <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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187 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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188 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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189 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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190 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
191 <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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192 <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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diff changeset
193 <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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194 <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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195 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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196 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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diff changeset
197 <section name="metrics">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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198 <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
199 <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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diff changeset
200 <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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201 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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202 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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203 </conditional>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
204 <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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205 <param name="header1" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 7
diff changeset
206 <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
207 <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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208 <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
209 <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"
bgruening
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diff changeset
210 <param name="save" value="save_weights" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
211 <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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diff changeset
212 <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
213 <has_n_columns n="2" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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214 </assert_contents>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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215 </output>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
216 <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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217 </test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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218 <test>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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219 <conditional name="experiment_schemes">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
220 <param name="selected_exp_scheme" value="train_test" />
14
0edcdeaad6f4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
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diff changeset
221 <param name="infile_estimator" value="pipeline10" ftype="h5mlm" />
0
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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222 <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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diff changeset
223 <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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224 <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
225 <param name="sp_value" value="10" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
226 <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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227 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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228 <repeat name="param_set">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 7
diff changeset
229 <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"
bgruening
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diff changeset
230 <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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231 </repeat>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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232 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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233 <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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234 <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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diff changeset
235 <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
236 <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
237 <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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238 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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239 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
240 <section name="metrics">
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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241 <conditional name="scoring">
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 7
diff changeset
242 <param name="primary_scoring" value="r2" />
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 7
diff changeset
243 <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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244 </conditional>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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245 </section>
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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246 </conditional>
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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247 <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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248 <param name="header1" value="true" />
8
f2c240cce242 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 7
diff changeset
249 <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
parents: 7
diff changeset
250 <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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251 <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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252 <param name="selected_column_selector_option2" value="all_columns" />
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253 <param name="save" value="nope" />
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254 <output name="outfile_result" file="train_test_eval03.tabular" />
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255 </test>
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256 </tests>
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257 <help>
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258 <![CDATA[
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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259 **What it does**
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260
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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261 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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262
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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263 - 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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264
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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265 - 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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266
39c06ed9be0a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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267 **Output**
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268
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269 Performance scores.
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270
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271 ]]>
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272 </help>
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273 <expand macro="sklearn_citation">
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274 <expand macro="skrebate_citation" />
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275 <expand macro="xgboost_citation" />
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276 <expand macro="keras_citation" />
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277 </expand>
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278 </tool>