Mercurial > repos > bgruening > sklearn_feature_selection
annotate feature_selection.xml @ 32:a7c667ff83fe draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d970dae980fbe349414fc0889f719d875d999c5b"
author | bgruening |
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date | Fri, 27 Aug 2021 10:19:00 +0000 |
parents | 93f3b307485f |
children | 61edd9e5c17f |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@" profile="20.05"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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3 <macros> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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4 <import>main_macros.xml</import> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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5 </macros> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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6 <expand macro="python_requirements" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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7 <!--TODO: Add imblearn package support--> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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8 <expand macro="macro_stdio" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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9 <version_command>echo "@VERSION@"</version_command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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10 <command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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11 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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12 python "$feature_selection_script" '$inputs' |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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13 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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14 </command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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15 <configfiles> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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16 <inputs name="inputs" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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17 <configfile name="feature_selection_script"> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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18 <![CDATA[ |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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19 import json |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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20 import sklearn.feature_selection |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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21 import skrebate |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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22 import pandas |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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23 import sys |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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24 import warnings |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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25 import xgboost |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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26 from sklearn import ( |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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27 cluster, compose, decomposition, ensemble, feature_extraction, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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28 feature_selection, gaussian_process, kernel_approximation, metrics, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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29 model_selection, naive_bayes, neighbors, pipeline, preprocessing, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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30 svm, linear_model, tree, discriminant_analysis) |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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31 from imblearn.pipeline import Pipeline as imbPipeline |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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32 from sklearn.pipeline import Pipeline |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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33 |
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34 from galaxy_ml.utils import (SafeEval, feature_selector, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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35 read_columns, get_module) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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36 |
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37 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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38 warnings.simplefilter('ignore') |
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39 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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40 safe_eval = SafeEval() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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41 |
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42 input_json_path = sys.argv[1] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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43 with open(input_json_path, 'r') as param_handler: |
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44 params = json.load(param_handler) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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45 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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46 ## handle cheetah |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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47 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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48 and $fs_algorithm_selector.model_inputter.input_mode == 'prefitted': |
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49 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\ |
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50 '$fs_algorithm_selector.model_inputter.fitted_estimator' |
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51 #end if |
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52 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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53 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\ |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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54 and $fs_algorithm_selector.model_inputter.input_mode == 'new'\ |
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55 and $fs_algorithm_selector.model_inputter.estimator_selector.selected_module == 'custom_estimator': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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56 params['fs_algorithm_selector']['model_inputter']['estimator_selector']['c_estimator'] =\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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57 '$fs_algorithm_selector.model_inputter.estimator_selector.c_estimator' |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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58 #end if |
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59 |
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60 #if $fs_algorithm_selector.selected_algorithm in ['RFE', 'RFECV', 'DyRFECV']\ |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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61 and $fs_algorithm_selector.estimator_selector.selected_module == 'custom_estimator': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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62 params['fs_algorithm_selector']['estimator_selector']['c_estimator'] =\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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63 '$fs_algorithm_selector.estimator_selector.c_estimator' |
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64 #end if |
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65 |
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66 #if $fs_algorithm_selector.selected_algorithm in ['RFECV', 'DyRFECV']\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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67 and $fs_algorithm_selector.options.cv_selector.selected_cv\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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68 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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69 params['fs_algorithm_selector']['options']['cv_selector']['groups_selector']['infile_g'] =\ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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70 '$fs_algorithm_selector.options.cv_selector.groups_selector.infile_g' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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71 #end if |
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72 |
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73 ## Read features |
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74 features_has_header = params['input_options']['header1'] |
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75 #if $input_options.selected_input == 'tabular' |
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76 header = 'infer' if features_has_header else None |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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77 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option'] |
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78 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']: |
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79 c = params['input_options']['column_selector_options_1']['col1'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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80 else: |
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81 c = None |
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82 X, input_df = read_columns( |
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83 '$input_options.infile1', |
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84 c = c, |
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85 c_option = column_option, |
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86 return_df = True, |
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87 sep='\t', |
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88 header=header, |
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89 parse_dates=True) |
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90 X = X.astype(float) |
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91 #elif $input_options.selected_input == 'seq_fasta' |
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92 fasta_file = '$input_options.fasta_file' |
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93 pyfaidx = get_module('pyfaidx') |
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94 sequences = pyfaidx.Fasta(fasta_file) |
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95 n_seqs = len(sequences.keys()) |
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96 X = np.arange(n_seqs)[:, np.newaxis] |
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97 for param in estimator_params.keys(): |
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98 if param.endswith('fasta_path'): |
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99 estimator.set_params( |
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100 **{param: fasta_file}) |
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101 else: |
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102 raise ValueError( |
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103 "The selected estimator doesn't support " |
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104 "fasta file input! Please consider using " |
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105 "KerasGBatchClassifier with " |
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106 "FastaDNABatchGenerator/FastaProteinBatchGenerator " |
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107 "or having GenomeOneHotEncoder/ProteinOneHotEncoder " |
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108 "in pipeline!") |
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109 #elif $input_options.selected_input == 'sparse' |
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110 X = mmread('$input_options.infile1') |
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111 #end if |
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112 |
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113 ## Read labels |
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114 header = 'infer' if params['input_options']['header2'] else None |
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115 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2'] |
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116 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']: |
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117 c = params['input_options']['column_selector_options_2']['col2'] |
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118 else: |
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119 c = None |
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120 y = read_columns( |
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121 '$input_options.infile2', |
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122 c = c, |
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123 c_option = column_option, |
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124 sep='\t', |
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125 header=header, |
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126 parse_dates=True) |
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127 y = y.ravel() |
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128 |
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129 ## Create feature selector |
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130 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y) |
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131 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\ |
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132 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' : |
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133 new_selector.fit(X, y) |
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134 |
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135 ## Transform to select features |
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136 selected_names = None |
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137 |
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138 res = new_selector.transform(X) |
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139 if features_has_header: |
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140 selected_names = input_df.columns[new_selector.get_support(indices=True)] |
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141 res = pandas.DataFrame(res, columns = selected_names) |
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142 res.to_csv(path_or_buf='$outfile', sep='\t', index=False) |
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143 |
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144 #if $save: |
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145 with open('$outfile_selector', 'wb') as output_handler: |
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146 pickle.dump(new_selector, output_handler, pickle.HIGHEST_PROTOCOL) |
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147 #end if |
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148 |
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149 ]]> |
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150 </configfile> |
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151 </configfiles> |
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152 <inputs> |
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153 <expand macro="feature_selection_fs" /> |
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154 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?" /> |
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155 <expand macro="sl_mixed_input_plus_sequence" /> |
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156 </inputs> |
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157 <outputs> |
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158 <data format="tabular" name="outfile" /> |
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159 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}"> |
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160 <filter>save</filter> |
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161 </data> |
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162 </outputs> |
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163 <tests> |
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164 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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165 <param name="selected_algorithm" value="SelectFromModel" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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166 <param name="input_mode" value="new" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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167 <param name="selected_module" value="ensemble" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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168 <param name="selected_estimator" value="RandomForestRegressor" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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169 <param name="text_params" value="n_estimators=10, random_state=10" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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170 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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171 <param name="header1" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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172 <param name="col1" value="1,2,3,4,5" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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173 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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174 <param name="col2" value="6" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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175 <param name="header2" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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176 <output name="outfile" file="feature_selection_result01" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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177 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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178 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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179 <param name="selected_algorithm" value="GenericUnivariateSelect" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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180 <param name="param" value="20" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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181 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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182 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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183 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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184 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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185 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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186 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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187 <output name="outfile" file="feature_selection_result02" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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188 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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189 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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190 <param name="selected_algorithm" value="SelectPercentile" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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191 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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192 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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193 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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194 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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195 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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196 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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197 <output name="outfile" file="feature_selection_result03" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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198 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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199 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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200 <param name="selected_algorithm" value="SelectKBest" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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201 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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202 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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203 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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204 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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205 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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206 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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207 <output name="outfile" file="feature_selection_result04" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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208 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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209 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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210 <param name="selected_algorithm" value="SelectFpr" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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211 <param name="alpha" value="0.05" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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212 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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213 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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214 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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215 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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216 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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217 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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218 <output name="outfile" file="feature_selection_result05" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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219 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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220 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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221 <param name="selected_algorithm" value="SelectFdr" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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222 <param name="alpha" value="0.05" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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223 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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224 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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225 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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226 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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227 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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228 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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229 <output name="outfile" file="feature_selection_result06" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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230 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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|
231 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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|
232 <param name="selected_algorithm" value="SelectFwe" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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|
233 <param name="alpha" value="0.05" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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234 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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|
235 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
236 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
237 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
238 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
239 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
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|
240 <output name="outfile" file="feature_selection_result07" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
241 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
242 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
243 <param name="selected_algorithm" value="RFE" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
244 <param name="input_mode" value="new" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
245 <param name="selected_module" value="ensemble" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
246 <param name="selected_estimator" value="RandomForestRegressor" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
247 <param name="text_params" value="n_estimators=10, random_state=10" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
248 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
249 <param name="header1" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
250 <param name="col1" value="1,2,3,4,5" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
251 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
252 <param name="col2" value="6" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
253 <param name="header2" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
254 <output name="outfile" file="feature_selection_result08" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
255 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
256 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
257 <param name="selected_algorithm" value="RFECV" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
258 <param name="input_mode" value="new" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
259 <param name="selected_module" value="ensemble" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
260 <param name="selected_estimator" value="RandomForestRegressor" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
261 <param name="text_params" value="n_estimators=10, random_state=10" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
262 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
263 <param name="header1" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
264 <param name="col1" value="1,2,3,4,5" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
265 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
266 <param name="col2" value="6" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
267 <param name="header2" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
268 <output name="outfile" file="feature_selection_result09" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
269 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
270 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
271 <param name="selected_algorithm" value="VarianceThreshold" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
272 <param name="threshold" value="0.1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
273 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
274 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
275 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
276 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
277 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
278 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
279 <output name="outfile" file="feature_selection_result10" /> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
280 </test> |
6
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
281 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
282 <param name="selected_algorithm" value="SelectKBest" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
283 <param name="k" value="3" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
284 <param name="infile1" value="test3.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
285 <param name="header1" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
286 <param name="selected_column_selector_option" value="all_but_by_header_name" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
287 <param name="col1" value="target" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
288 <param name="infile2" value="test3.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
289 <param name="header2" value="True" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
290 <param name="selected_column_selector_option2" value="by_header_name" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
291 <param name="col2" value="target" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
292 <output name="outfile" file="feature_selection_result11" /> |
6
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
293 </test> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
294 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
295 <param name="selected_algorithm" value="SelectFromModel" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
296 <param name="input_mode" value="prefitted" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
297 <param name="fitted_estimator" value="rfr_model01" ftype="zip" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
298 <param name="infile1" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
299 <param name="header1" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
300 <param name="col1" value="1,2,3,4,5" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
301 <param name="infile2" value="regression_train.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
302 <param name="col2" value="1" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
303 <param name="header2" value="false" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
304 <output name="outfile" file="feature_selection_result12" /> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
305 </test> |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
306 <test> |
29
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
307 <param name="selected_algorithm" value="RFECV" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
308 <param name="input_mode" value="new" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
309 <param name="selected_module" value="ensemble" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
310 <param name="selected_estimator" value="RandomForestRegressor" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
311 <param name="text_params" value="n_estimators=10, random_state=10" /> |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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312 <section name="groups_selector"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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313 <param name="infile_groups" value="regression_y.tabular" ftype="tabular" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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314 <param name="header_g" value="true" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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315 <param name="selected_column_selector_option_g" value="by_index_number" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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316 <param name="col_g" value="1" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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317 </section> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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318 <param name="selected_cv" value="GroupShuffleSplit" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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319 <param name="random_state" value="0" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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320 <param name="infile1" value="regression_X.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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321 <param name="header1" value="true" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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322 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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323 <param name="infile2" value="regression_y.tabular" ftype="tabular" /> |
93f3b307485f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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324 <param name="col2" value="1" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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325 <param name="header2" value="true" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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326 <output name="outfile" file="feature_selection_result13" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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327 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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328 </tests> |
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329 <help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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330 <![CDATA[ |
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331 **What it does** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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332 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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333 sklearn.metrics package. |
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334 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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335 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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336 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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337 ]]> |
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338 </help> |
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339 <expand macro="sklearn_citation"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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340 <expand macro="skrebate_citation" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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341 <expand macro="xgboost_citation" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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342 </expand> |
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343 </tool> |