Mercurial > repos > bgruening > keras_train_and_eval
annotate keras_train_and_eval.xml @ 10:b3093f953091 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author | bgruening |
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date | Wed, 09 Aug 2023 13:30:51 +0000 |
parents | 3866911c93ae |
children | 818f9b69d8a0 |
rev | line source |
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10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
diff
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1 <tool id="keras_train_and_eval" name="Deep learning training and evaluation" version="@VERSION@" profile="@PROFILE@"> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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2 <description>conduct deep training and evaluation either implicitly or explicitly</description> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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3 <macros> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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4 <import>main_macros.xml</import> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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5 <import>keras_macros.xml</import> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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6 </macros> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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7 <expand macro="python_requirements" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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8 <expand macro="macro_stdio" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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9 <version_command>echo "@VERSION@"</version_command> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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10 <command> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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11 <![CDATA[ |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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12 export HDF5_USE_FILE_LOCKING='FALSE'; |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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13 #if $input_options.selected_input == 'refseq_and_interval' |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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14 bgzip -c '$input_options.target_file' > '${target_file.element_identifier}.gz' && |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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15 tabix -p bed '${target_file.element_identifier}.gz' && |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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16 cp '$input_options.ref_genome_file' '${ref_genome_file.element_identifier}' && |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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17 #end if |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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18 python '$__tool_directory__/keras_train_and_eval.py' |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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19 --inputs '$inputs' |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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20 --estimator '$experiment_schemes.infile_estimator' |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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21 #if $input_options.selected_input == 'seq_fasta' |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
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22 --fasta_path '$input_options.fasta_path' |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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23 #elif $input_options.selected_input == 'refseq_and_interval' |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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24 --ref_seq "`pwd`/${ref_genome_file.element_identifier}" |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
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25 --interval '$input_options.interval_file' |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
diff
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26 --targets "`pwd`/${target_file.element_identifier}.gz" |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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27 #else |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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28 --infile1 '$input_options.infile1' |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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29 #end if |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
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30 --infile2 '$input_options.infile2' |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
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31 --outfile_result '$outfile_result' |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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32 #if $save and 'save_estimator' in str($save) |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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33 --outfile_object '$outfile_object' |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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34 #end if |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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35 #if $save and 'save_prediction' in str($save) |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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36 --outfile_y_true '$outfile_y_true' |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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37 --outfile_y_preds '$outfile_y_preds' |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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38 #end if |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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39 #if $experiment_schemes.test_split.split_algos.shuffle == 'group' |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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40 --groups '$experiment_schemes.test_split.split_algos.groups_selector.infile_g' |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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41 #end if |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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42 |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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43 ]]> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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44 </command> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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45 <configfiles> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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46 <inputs name="inputs" /> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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47 </configfiles> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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48 <inputs> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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49 <conditional name="experiment_schemes"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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50 <param name="selected_exp_scheme" type="select" label="Select a scheme"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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51 <option value="train_val" selected="true">Train and Validate</option> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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52 <option value="train_val_test">Train, Validate and and Evaluate</option> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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53 </param> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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54 <when value="train_val"> |
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3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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55 <expand macro="estimator_and_hyperparameter" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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56 <section name="test_split" title="Validation holdout" expanded="false"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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57 <expand macro="train_test_split_params"> |
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3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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58 <expand macro="cv_groups" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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59 </expand> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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60 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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61 <section name="metrics" title="Metrics for evaluation" expanded="false"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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62 <expand macro="scoring_selection" help="" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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63 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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64 </when> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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65 <when value="train_val_test"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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66 <expand macro="estimator_and_hyperparameter" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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67 <section name="test_split" title="Test holdout" expanded="false"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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68 <expand macro="train_test_split_params"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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69 <expand macro="cv_groups" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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70 </expand> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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71 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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72 <section name="val_split" title="Validation holdout (recommend using the same splitting method as for test holdout)" expanded="false"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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73 <expand macro="train_test_split_params" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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74 </section> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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75 <section name="metrics" title="Metrics from scikit-learn" expanded="false"> |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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76 <expand macro="scoring_selection" help="" /> |
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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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77 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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78 </when> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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79 </conditional> |
4
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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80 <expand macro="sl_mixed_input_plus_sequence" /> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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81 <param name="save" type="select" multiple='true' display="checkboxes" label="Save the fitted model" optional="true" help="Evaluation scores will be output by default."> |
10
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82 <option value="save_estimator" selected="true">Fitted estimator</option> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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83 <option value="save_prediction">True labels and prediction results from evaluation for downstream analysis</option> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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84 </param> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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85 </inputs> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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86 <outputs> |
4
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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87 <data format="tabular" name="outfile_result" /> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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88 <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
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89 <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
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90 </data> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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91 <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
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92 <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
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93 </data> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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94 <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
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95 <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
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96 </data> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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97 </outputs> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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98 <tests> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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99 <test> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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100 <conditional name="experiment_schemes"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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101 <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
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102 <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
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103 <section name="hyperparams_swapping"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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104 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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105 <param name="sp_value" value="999" /> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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106 <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
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107 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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108 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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109 <param name="sp_value" value="999" /> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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110 <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:
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111 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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112 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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113 <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
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114 <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
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115 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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116 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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117 <param name="sp_value" value="'adamax'" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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118 <param name="sp_name" value="optimizer" /> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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119 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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120 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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121 <section name="test_split"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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122 <conditional name="split_algos"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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123 <param name="shuffle" value="simple" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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124 <param name="test_size" value="0.2" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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125 <param name="random_state" value="123" /> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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126 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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127 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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128 <section name="val_split"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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129 <conditional name="split_algos"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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130 <param name="shuffle" value="simple" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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131 <param name="test_size" value="0.2" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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132 <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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133 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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134 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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135 <section name="metrics"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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136 <conditional name="scoring"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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137 <param name="primary_scoring" value="r2" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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138 <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
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139 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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140 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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141 </conditional> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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142 <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
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143 <param name="header1" value="true" /> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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144 <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
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2
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|
145 <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
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146 <param name="header2" value="true" /> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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147 <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
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|
148 <param name="save" value="save_estimator" /> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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149 <output name="outfile_result"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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150 <assert_contents> |
10
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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|
151 <has_n_columns n="4" /> |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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|
152 <has_text text="0.794" /> |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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|
153 <has_text text="-4.62" /> |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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154 </assert_contents> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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155 </output> |
10
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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|
156 <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
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|
157 </test> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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|
158 <test> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
159 <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
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|
160 <param name="selected_exp_scheme" value="train_val_test" /> |
10
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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161 <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
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162 <section name="hyperparams_swapping"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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163 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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164 <param name="sp_value" value="999" /> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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165 <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:
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166 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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167 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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168 <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:
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169 <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:
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170 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
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171 <repeat name="param_set"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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172 <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:
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173 <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
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174 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
175 <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
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|
176 <param name="sp_value" value="'adamax'" /> |
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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177 <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:
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178 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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179 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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180 <section name="test_split"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
181 <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
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|
182 <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
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|
183 <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
|
184 <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
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|
185 <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
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|
186 <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
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|
187 <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
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|
188 <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
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189 <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:
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190 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
191 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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192 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
193 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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194 <section name="val_split"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
195 <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
|
196 <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
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|
197 <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:
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198 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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199 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
200 <section name="metrics"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
201 <conditional name="scoring"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
2
diff
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|
202 <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
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|
203 <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:
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|
204 </conditional> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
205 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
206 </conditional> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
2
diff
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|
207 <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:
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|
208 <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
|
209 <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
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|
210 <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
|
211 <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
|
212 <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
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|
213 <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
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|
214 <output name="outfile_result" > |
0
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
215 <assert_contents> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
diff
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|
216 <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
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|
217 <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
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|
218 <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
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|
219 </assert_contents> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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|
220 </output> |
10
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
4
diff
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|
221 <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
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|
222 <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:
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changeset
|
223 </test> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
224 <test> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
225 <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
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|
226 <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
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|
227 <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
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|
228 <section name="hyperparams_swapping"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
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|
229 <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
|
230 <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
|
231 <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
|
232 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
233 <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
|
234 <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
|
235 <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
|
236 </repeat> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
237 </section> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
238 <section name="test_split"> |
03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff
changeset
|
239 <conditional name="split_algos"> |
4
3866911c93ae
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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240 <param name="shuffle" value="simple" /> |
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241 <param name="test_size" value="0.2" /> |
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242 <param name="random_state" value="123" /> |
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243 </conditional> |
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244 </section> |
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245 <section name="val_split"> |
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246 <conditional name="split_algos"> |
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247 <param name="shuffle" value="simple" /> |
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248 <param name="test_size" value="0.2" /> |
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249 <param name="random_state" value="456" /> |
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250 </conditional> |
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251 </section> |
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252 <section name="metrics"> |
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253 <conditional name="scoring"> |
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254 <param name="primary_scoring" value="r2" /> |
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255 <param name="secondary_scoring" value="neg_mean_absolute_error" /> |
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256 </conditional> |
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257 </section> |
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258 </conditional> |
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259 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
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260 <param name="header1" value="true" /> |
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261 <param name="selected_column_selector_option" value="all_columns" /> |
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262 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
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263 <param name="header2" value="true" /> |
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264 <param name="selected_column_selector_option2" value="all_columns" /> |
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265 <param name="save" value="" /> |
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266 <output name="outfile_result" file="train_test_eval03.tabular" /> |
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267 </test> |
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268 </tests> |
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269 <help> |
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270 <![CDATA[ |
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271 **What it does** |
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272 |
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273 Given a pre-built keras deep learning model and labeled training dataset, this tool works in two modes. |
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274 |
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275 - 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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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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276 |
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277 |
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278 - 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. |
b3093f953091
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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279 |
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280 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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281 |
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282 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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283 |
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284 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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03f61bb3ca43
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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285 |
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286 **Input** |
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287 |
03f61bb3ca43
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288 - tabular |
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289 - sparse |
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290 - `sequences in a fasta file` to work with DNA, RNA and proteins with corresponding fasta data generator |
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291 - `reference genome and intervals` exclusively work with `GenomicIntervalBatchGenerator`. |
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292 |
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293 **Output** |
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294 |
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295 - performance scores from evaluation |
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296 - fitted estimator |
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297 - true labels or values and predicted values from the evaluation |
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298 |
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299 ]]> |
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300 </help> |
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301 <expand macro="sklearn_citation"> |
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302 <expand macro="keras_citation" /> |
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303 </expand> |
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304 </tool> |