annotate keras_train_and_eval.xml @ 16:2af1346e68c9 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 15:43:41 +0000
parents 818f9b69d8a0
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1 <tool id="keras_train_and_eval" name="Deep learning training and evaluation" version="@VERSION@" profile="@PROFILE@">
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2 <description>conduct deep training and evaluation either implicitly or explicitly</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>
4
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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>
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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 cp '$input_options.ref_genome_file' '${ref_genome_file.element_identifier}' &&
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17 #end if
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18 python '$__tool_directory__/keras_train_and_eval.py'
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19 --inputs '$inputs'
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20 --estimator '$experiment_schemes.infile_estimator'
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21 #if $input_options.selected_input == 'seq_fasta'
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22 --fasta_path '$input_options.fasta_path'
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23 #elif $input_options.selected_input == 'refseq_and_interval'
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24 --ref_seq "`pwd`/${ref_genome_file.element_identifier}"
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25 --interval '$input_options.interval_file'
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26 --targets "`pwd`/${target_file.element_identifier}.gz"
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27 #else
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28 --infile1 '$input_options.infile1'
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29 #end if
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30 --infile2 '$input_options.infile2'
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31 --outfile_result '$outfile_result'
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32 #if $save and 'save_csvlogger' in str($save)
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33 --outfile_history '$outfile_history'
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34 #end if
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35 #if $save and 'save_estimator' in str($save)
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36 --outfile_object '$outfile_object'
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37 #end if
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38 #if $save and 'save_prediction' in str($save)
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39 --outfile_y_true '$outfile_y_true'
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40 --outfile_y_preds '$outfile_y_preds'
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41 #end if
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42 #if $experiment_schemes.test_split.split_algos.shuffle == 'group'
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43 --groups '$experiment_schemes.test_split.split_algos.groups_selector.infile_g'
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44 #end if
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45 ]]>
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46 </command>
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47 <configfiles>
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48 <inputs name="inputs" />
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49 </configfiles>
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50 <inputs>
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51 <conditional name="experiment_schemes">
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52 <param name="selected_exp_scheme" type="select" label="Select a scheme">
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53 <option value="train_val" selected="true">Train and Validate</option>
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54 <option value="train_val_test">Train, Validate and and Evaluate</option>
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55 </param>
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56 <when value="train_val">
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57 <expand macro="estimator_and_hyperparameter" />
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58 <section name="test_split" title="Validation holdout" expanded="false">
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59 <expand macro="train_test_split_params">
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60 <expand macro="cv_groups" />
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61 </expand>
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62 </section>
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63 <section name="metrics" title="Metrics for evaluation" expanded="false">
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64 <expand macro="scoring_selection" help="" />
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65 </section>
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66 </when>
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67 <when value="train_val_test">
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68 <expand macro="estimator_and_hyperparameter" />
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69 <section name="test_split" title="Test holdout" expanded="false">
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70 <expand macro="train_test_split_params">
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71 <expand macro="cv_groups" />
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72 </expand>
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73 </section>
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74 <section name="val_split" title="Validation holdout (recommend using the same splitting method as for test holdout)" expanded="false">
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75 <expand macro="train_test_split_params" />
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76 </section>
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77 <section name="metrics" title="Metrics from scikit-learn" expanded="false">
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78 <expand macro="scoring_selection" help="" />
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79 </section>
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80 </when>
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81 </conditional>
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82 <expand macro="sl_mixed_input_plus_sequence" />
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83 <param name="save" type="select" multiple='true' display="checkboxes" label="Save the fitted model" optional="true" help="Evaluation scores will be output by default.">
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84 <option value="save_estimator" selected="true">Fitted estimator</option>
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85 <option value="save_prediction">True labels and prediction results from evaluation for downstream analysis</option>
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86 <option value="save_csvlogger">Display CSVLogger if selected as a callback in the Keras model builder tool</option>
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
87 </param>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
88 </inputs>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
89 <outputs>
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
90 <data format="tabular" name="outfile_result" />
14
818f9b69d8a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 10
diff changeset
91 <data format="tabular" name="outfile_history" label="Deep learning training history log on ${on_string}">
818f9b69d8a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 10
diff changeset
92 <filter>str(save) and 'save_csvlogger' in str(save)</filter>
818f9b69d8a0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 10
diff changeset
93 </data>
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
94 <data format="h5mlm" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
95 <filter>str(save) and 'save_estimator' in str(save)</filter>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
96 </data>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
97 <data format="tabular" name="outfile_y_true" label="True labels/target values on ${on_string}">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
98 <filter>str(save) and 'save_prediction' in str(save)</filter>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
99 </data>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
100 <data format="tabular" name="outfile_y_preds" label="All predictions on ${on_string}">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
101 <filter>str(save) and 'save_prediction' in str(save)</filter>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
102 </data>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
103 </outputs>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
104 <tests>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
105 <test>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
106 <conditional name="experiment_schemes">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
107 <param name="selected_exp_scheme" value="train_val_test" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
108 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
109 <section name="hyperparams_swapping">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
110 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
111 <param name="sp_value" value="999" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
112 <param name="sp_name" value="layers_1_Dense__config__kernel_initializer__config__seed" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
113 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
114 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
115 <param name="sp_value" value="999" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
116 <param name="sp_name" value="layers_3_Dense__config__kernel_initializer__config__seed" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
117 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
118 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
119 <param name="sp_value" value="0.1" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
120 <param name="sp_name" value="learning_rate" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
121 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
122 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
123 <param name="sp_value" value="'adamax'" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
124 <param name="sp_name" value="optimizer" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
125 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
126 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
127 <section name="test_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
128 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
129 <param name="shuffle" value="simple" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
130 <param name="test_size" value="0.2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
131 <param name="random_state" value="123" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
132 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
133 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
134 <section name="val_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
135 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
136 <param name="shuffle" value="simple" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
137 <param name="test_size" value="0.2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
138 <param name="random_state" value="456" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
139 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
140 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
141 <section name="metrics">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
142 <conditional name="scoring">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
143 <param name="primary_scoring" value="r2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
144 <param name="secondary_scoring" value="neg_mean_absolute_error" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
145 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
146 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
147 </conditional>
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
148 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
149 <param name="header1" value="true" />
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
150 <param name="selected_column_selector_option" value="all_columns" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
151 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
152 <param name="header2" value="true" />
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
153 <param name="selected_column_selector_option2" value="all_columns" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
154 <param name="save" value="save_estimator" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
155 <output name="outfile_result">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
156 <assert_contents>
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
157 <has_n_columns n="4" />
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
158 <has_text text="0.794" />
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
159 <has_text text="-4.62" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
160 </assert_contents>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
161 </output>
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
162 <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="5" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
163 </test>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
164 <test>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
165 <conditional name="experiment_schemes">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
166 <param name="selected_exp_scheme" value="train_val_test" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
167 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
168 <section name="hyperparams_swapping">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
169 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
170 <param name="sp_value" value="999" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
171 <param name="sp_name" value="layers_1_Dense__config__kernel_initializer__config__seed" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
172 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
173 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
174 <param name="sp_value" value="999" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
175 <param name="sp_name" value="layers_3_Dense__config__kernel_initializer__config__seed" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
176 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
177 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
178 <param name="sp_value" value="0.1" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
179 <param name="sp_name" value="learning_rate" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
180 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
181 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
182 <param name="sp_value" value="'adamax'" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
183 <param name="sp_name" value="optimizer" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
184 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
185 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
186 <section name="test_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
187 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
188 <param name="shuffle" value="group" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
189 <param name="group_names" value="test" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
190 <section name="groups_selector">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
191 <param name="infile_g" value="regression_groups.tabular" ftype="tabular" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
192 <param name="header_g" value="true" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
193 <conditional name="column_selector_options_g">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
194 <param name="selected_column_selector_option_g" value="by_index_number" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
195 <param name="col_g" value="1" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
196 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
197 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
198 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
199 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
200 <section name="val_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
201 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
202 <param name="shuffle" value="group" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
203 <param name="group_names" value="validation" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
204 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
205 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
206 <section name="metrics">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
207 <conditional name="scoring">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
208 <param name="primary_scoring" value="r2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
209 <param name="secondary_scoring" value="neg_mean_absolute_error" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
210 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
211 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
212 </conditional>
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
213 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
214 <param name="header1" value="true" />
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
215 <param name="selected_column_selector_option" value="all_columns" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
216 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
217 <param name="header2" value="true" />
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
218 <param name="selected_column_selector_option2" value="all_columns" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
219 <param name="save" value="save_estimator,save_prediction" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
220 <output name="outfile_result" >
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
221 <assert_contents>
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
222 <has_n_columns n="4" />
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
223 <has_text text="0.779" />
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
224 <has_text text="-4.5" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
225 </assert_contents>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
226 </output>
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
227 <output name="outfile_object" file="train_test_eval_model02" compare="sim_size" delta="5" />
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
228 <output name="outfile_y_true" file="keras_train_eval_y_true02.tabular" ftype="tabular" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
229 </test>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
230 <test>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
231 <conditional name="experiment_schemes">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
232 <param name="selected_exp_scheme" value="train_val" />
10
b3093f953091 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 4
diff changeset
233 <param name="infile_estimator" value="pipeline10" ftype="h5mlm" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
234 <section name="hyperparams_swapping">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
235 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
236 <param name="sp_value" value="10" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
237 <param name="sp_name" value="adaboostregressor__random_state" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
238 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
239 <repeat name="param_set">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
240 <param name="sp_value" value=": sklearn_tree.ExtraTreeRegressor(random_state=0)" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
241 <param name="sp_name" value="adaboostregressor__base_estimator" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
242 </repeat>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
243 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
244 <section name="test_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
245 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
246 <param name="shuffle" value="simple" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
247 <param name="test_size" value="0.2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
248 <param name="random_state" value="123" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
249 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
250 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
251 <section name="val_split">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
252 <conditional name="split_algos">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
253 <param name="shuffle" value="simple" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
254 <param name="test_size" value="0.2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
255 <param name="random_state" value="456" />
0
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
256 </conditional>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
257 </section>
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
258 <section name="metrics">
03f61bb3ca43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
259 <conditional name="scoring">
4
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 2
diff changeset
260 <param name="primary_scoring" value="r2" />
3866911c93ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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261 <param name="secondary_scoring" value="neg_mean_absolute_error" />
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262 </conditional>
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263 </section>
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264 </conditional>
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265 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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266 <param name="header1" value="true" />
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267 <param name="selected_column_selector_option" value="all_columns" />
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268 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
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269 <param name="header2" value="true" />
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270 <param name="selected_column_selector_option2" value="all_columns" />
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271 <param name="save" value="" />
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272 <output name="outfile_result" file="train_test_eval03.tabular" />
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273 </test>
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274 </tests>
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275 <help>
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276 <![CDATA[
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277 **What it does**
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278
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279 Given a pre-built keras deep learning model and labeled training dataset, this tool works in two modes.
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280
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281 - Train and Validate: the intput dataset is split into training and validation portions. The model is fitted on the training portion, in the meantime performances are evaluated on the validation portion multiple times while the training is progressing. Finally, a fitted model and its validation performance scores are outputted.
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282
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283
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284 - Train, Validate and and Evaluate: the input dataset is split into three portions, training, validation and testing. The same `Train and Validate` described above is performed on the training and validation portions. The testing portion is used exclusively for testing (evaluation). As a result, a fitted model and test performance scores are outputted.
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285
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286 In both modes, besides the performance scores, the true labels and predicted values are outputted, which could be used in generating plots in other tools, machine learning visualization extensions, for example.
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287
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288 Note that since all training and model parameters are accessible and changeable in the `Hyperparameter Swapping` section, the training and evaluation processes are flexible and transparent.
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289
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290 For metrics, there are two sets of metrics for deep learning training and evaluation, one from the keras model builder and the other from scikit-learn. Keras metrics, if selected, are always evaluated, while the sklearn metrics could be ignored when `default` is the selection. Please be aware that not every sklearn metric works with deep learning model at current moment. Feel free to file a ticket if an issue is found and contibuting with PRs is always welcomed.
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291
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292 **Input**
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293
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294 - tabular
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295 - sparse
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296 - `sequences in a fasta file` to work with DNA, RNA and proteins with corresponding fasta data generator
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297 - `reference genome and intervals` exclusively work with `GenomicIntervalBatchGenerator`.
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298
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299 **Output**
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300
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301 - performance scores from evaluation
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302 - fitted estimator
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303 - true labels or values and predicted values from the evaluation
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304
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305 ]]>
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306 </help>
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307 <expand macro="sklearn_citation">
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308 <expand macro="keras_citation" />
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309 </expand>
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310 </tool>