Mercurial > repos > bgruening > sklearn_build_pipeline
annotate pipeline.xml @ 8:913ee94945f3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author | bgruening |
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date | Tue, 14 May 2019 18:06:37 -0400 |
parents | 99038af8deda |
children | 775b004b7920 |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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1 <tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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2 <description>constructs a list of transforms and a final estimator</description> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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3 <macros> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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4 <import>main_macros.xml</import> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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5 </macros> |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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6 <expand macro="python_requirements"/> |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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7 <expand macro="macro_stdio"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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8 <version_command>echo "@VERSION@"</version_command> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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9 <command> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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10 <![CDATA[ |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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11 python "$sklearn_pipeline_script" '$inputs' |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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12 ]]> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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13 </command> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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14 <configfiles> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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15 <inputs name="inputs" /> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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16 <configfile name="sklearn_pipeline_script"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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17 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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18 import imblearn |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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19 import json |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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20 import pickle |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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21 import pprint |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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22 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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23 import sys |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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24 import warnings |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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25 from mlxtend import classifier, regressor |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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26 from sklearn import ( |
913ee94945f3
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, |
913ee94945f3
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, |
913ee94945f3
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, |
913ee94945f3
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) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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31 from sklearn.pipeline import make_pipeline |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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32 from imblearn.pipeline import make_pipeline as imb_make_pipeline |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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33 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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34 sys.path.insert(0, '$__tool_directory__') |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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35 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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36 from utils import SafeEval, feature_selector, get_estimator, try_get_attr |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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37 from preprocessors import Z_RandomOverSampler |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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38 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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39 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1)) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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40 |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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41 warnings.filterwarnings('ignore') |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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42 |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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43 safe_eval = SafeEval() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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44 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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45 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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46 with open(input_json_path, 'r') as param_handler: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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47 params = json.load(param_handler) |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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48 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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49 #if $final_estimator.estimator_selector.selected_module == 'custom_estimator': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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50 params['final_estimator']['estimator_selector']['c_estimator'] =\ |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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51 '$final_estimator.estimator_selector.c_estimator' |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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52 #end if |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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53 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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54 #if $final_estimator.estimator_selector.selected_module == 'binarize_target': |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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55 params['final_estimator']['estimator_selector']['wrapped_estimator'] =\ |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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56 '$final_estimator.estimator_selector.wrapped_estimator' |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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57 #end if |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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58 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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59 pipeline_steps = [] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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60 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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61 def get_component(input_json, check_none=False): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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62 is_imblearn = False |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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63 if input_json['component_type'] == 'None': |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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64 if not check_none: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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65 return None, False |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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66 else: |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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67 sys.exit("The pre-processing component type can't be None " |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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68 "when the number of components is greater than 1.") |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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69 if input_json['component_type'] == 'pre_processor': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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70 preprocessor = input_json['pre_processors']['selected_pre_processor'] |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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71 pre_processor_options = input_json['pre_processors']['options'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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72 my_class = getattr(preprocessing, preprocessor) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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73 obj = my_class(**pre_processor_options) |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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74 elif input_json['component_type'] == 'feature_selection': |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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75 obj = feature_selector(input_json['fs_algorithm_selector']) |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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76 elif input_json['component_type'] == 'decomposition': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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77 algorithm = input_json['matrix_decomposition_selector']['select_algorithm'] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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78 obj = getattr(decomposition, algorithm)() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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79 options = input_json['matrix_decomposition_selector']['text_params'].strip() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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80 if options != '': |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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81 options = safe_eval( 'dict(' + options + ')' ) |
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82 obj.set_params(**options) |
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83 elif input_json['component_type'] == 'kernel_approximation': |
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84 algorithm = input_json['kernel_approximation_selector']['select_algorithm'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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85 obj = getattr(kernel_approximation, algorithm)() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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86 options = input_json['kernel_approximation_selector']['text_params'].strip() |
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87 if options != '': |
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88 options = safe_eval( 'dict(' + options + ')' ) |
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89 obj.set_params(**options) |
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90 elif input_json['component_type'] == 'FeatureAgglomeration': |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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91 algorithm = input_json['FeatureAgglomeration_selector']['select_algorithm'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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92 obj = getattr(cluster, algorithm)() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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93 options = input_json['FeatureAgglomeration_selector']['text_params'].strip() |
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94 if options != '': |
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95 options = safe_eval( 'dict(' + options + ')' ) |
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96 obj.set_params(**options) |
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97 elif input_json['component_type'] == 'skrebate': |
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98 algorithm = input_json['skrebate_selector']['select_algorithm'] |
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99 if algorithm == 'TuRF': |
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100 obj = getattr(skrebate, algorithm)(core_algorithm='ReliefF') |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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101 else: |
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102 obj = getattr(skrebate, algorithm)() |
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103 options = input_json['skrebate_selector']['text_params'].strip() |
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104 if options != '': |
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105 options = safe_eval( 'dict(' + options + ')' ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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106 obj.set_params(**options) |
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107 elif input_json['component_type'] == 'imblearn': |
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108 is_imblearn = True |
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109 algorithm = input_json['imblearn_selector']['select_algorithm'] |
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110 if algorithm == 'over_sampling.SMOTENC': |
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111 obj = over_sampling.SMOTENC(categorical_features=[]) |
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112 elif algorithm == 'Z_RandomOverSampler': |
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113 obj = Z_RandomOverSampler() |
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114 else: |
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115 globals = algorithm.split('.') |
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116 mod, klass = globals[0], globals[1] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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117 obj = getattr(getattr(imblearn, mod), klass)() |
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118 options = input_json['imblearn_selector']['text_params'].strip() |
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119 if options != '': |
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120 options = safe_eval( 'dict(' + options + ')' ) |
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121 obj.set_params(**options) |
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122 elif input_json['component_type'] == 'IRAPS': |
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123 iraps_core = try_get_attr('iraps_classifier','IRAPSCore')() |
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124 core_params = input_json['text_params'].strip() |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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125 if core_params != '': |
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126 try: |
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127 params = safe_eval('dict(' + core_params + ')') |
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128 except ValueError: |
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129 sys.exit("Unsupported parameter input: `%s`" % core_params) |
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130 iraps_core.set_params(**params) |
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131 options = {} |
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132 if input_json['p_thres'] is not None: |
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133 options['p_thres'] = input_json['p_thres'] |
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134 if input_json['fc_thres'] is not None: |
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135 options['fc_thres'] = input_json['fc_thres'] |
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136 if input_json['occurrence'] is not None: |
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137 options['occurrence'] = input_json['occurrence'] |
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138 if input_json['discretize'] is not None: |
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139 options['discretize'] = input_json['discretize'] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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140 IRAPSClassifier = try_get_attr('iraps_classifier','IRAPSClassifier') |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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141 obj = IRAPSClassifier(iraps_core, **options) |
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142 if 'n_jobs' in obj.get_params(): |
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143 obj.set_params( n_jobs=N_JOBS ) |
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144 return obj, is_imblearn |
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145 |
7
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146 has_imblearn = False |
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147 if len(params['pipeline_component']) == 1: |
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148 step_obj, is_imblearn = get_component( params['pipeline_component'][0]['component_selector']) |
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149 if step_obj: |
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150 pipeline_steps.append( step_obj ) |
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151 if is_imblearn: |
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152 has_imblearn = True |
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153 else: |
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154 for i, c in enumerate(params['pipeline_component']): |
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155 step_obj, is_imblearn = get_component( c['component_selector'], check_none=True ) |
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156 pipeline_steps.append( step_obj ) |
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157 if is_imblearn: |
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158 has_imblearn = True |
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159 |
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160 ## Set up final estimator and add to pipeline. |
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161 estimator_json = params['final_estimator']['estimator_selector'] |
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162 if estimator_json['selected_module'] == 'none': |
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163 if len(pipeline_steps) == 0: |
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164 sys.exit("No pipeline steps specified!") |
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165 ## else: turn the last pre-process component to final estimator |
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166 else: |
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167 estimator = get_estimator(estimator_json) |
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168 pipeline_steps.append( estimator ) |
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169 |
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170 #if $output_type == 'Final_Estimator_Builder': |
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171 with open('$outfile', 'wb') as out_handler: |
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172 final_est = pipeline_steps[-1] |
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173 print(final_est) |
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174 pickle.dump(final_est, out_handler, pickle.HIGHEST_PROTOCOL) |
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175 #else: |
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176 if has_imblearn: |
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177 pipeline = imb_make_pipeline(*pipeline_steps) |
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178 else: |
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179 pipeline = make_pipeline(*pipeline_steps) |
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180 pprint.pprint(pipeline.named_steps) |
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181 |
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182 with open('$outfile', 'wb') as out_handler: |
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183 pickle.dump(pipeline, out_handler, pickle.HIGHEST_PROTOCOL) |
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184 #end if |
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185 ]]> |
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186 </configfile> |
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187 </configfiles> |
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188 <inputs> |
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189 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step"> |
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190 <conditional name="component_selector"> |
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191 <param name="component_type" type="select" label="Choose the type of transformation:"> |
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192 <option value="None" selected="true">None</option> |
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193 <option value="pre_processor">Sklearn Preprocessor</option> |
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194 <option value="feature_selection">Feature Selection</option> |
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195 <option value="decomposition">Matrix Decomposition</option> |
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196 <option value="kernel_approximation">Kernel Approximation</option> |
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197 <option value="FeatureAgglomeration">Agglomerate Features</option> |
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198 <option value="skrebate">SK-rebate feature selection</option> |
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199 <option value="imblearn">imbalanced-learn sampling</option> |
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200 <option value="IRAPS">IRAPS -- feature selector and classifier</option> |
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201 </param> |
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202 <when value="None"/> |
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203 <when value="pre_processor"> |
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204 <conditional name="pre_processors"> |
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205 <expand macro="sparse_preprocessors_ext" /> |
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206 <expand macro="sparse_preprocessor_options_ext" /> |
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207 </conditional> |
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208 </when> |
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209 <when value="feature_selection"> |
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210 <expand macro="feature_selection_pipeline"/> |
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211 </when> |
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212 <when value="decomposition"> |
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213 <expand macro="matrix_decomposition_all"/> |
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214 </when> |
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215 <when value="kernel_approximation"> |
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216 <expand macro="kernel_approximation_all"/> |
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217 </when> |
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218 <when value="FeatureAgglomeration"> |
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219 <expand macro="FeatureAgglomeration"/> |
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220 </when> |
3
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221 <when value="skrebate"> |
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222 <expand macro="skrebate"/> |
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223 </when> |
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224 <when value="imblearn"> |
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225 <expand macro="imbalanced_learn_sampling"/> |
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226 </when> |
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227 <when value="IRAPS"> |
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228 <expand macro="estimator_params_text" |
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229 label="Type in parameter settings for IRAPSCore if different from default:" |
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230 help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes"/> |
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231 <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001"/> |
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232 <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1"/> |
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233 <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7"/> |
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234 <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1"/> |
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235 </when> |
0
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236 </conditional> |
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237 </repeat> |
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238 <section name="final_estimator" title="Final Estimator" expanded="true"> |
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239 <conditional name="estimator_selector"> |
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240 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > |
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241 <expand macro="estimator_module_options"> |
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242 <option value="binarize_target">Binarize Target Classifier or Regressor</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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243 <option value="custom_estimator">Load a custom estimator</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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244 <option value="none">none -- The last component of pre-processing step will turn to a final estimator</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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245 </expand> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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246 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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247 <expand macro="estimator_suboptions"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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248 <when value="binarize_target"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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249 <param name="clf_or_regr" type="select" label="Classifier or Regressor:"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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250 <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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251 <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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252 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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253 <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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254 <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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255 <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None."/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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256 <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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257 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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258 <when value="custom_estimator"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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259 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/> |
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260 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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261 <when value="none"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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262 </expand> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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263 </conditional> |
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264 </section> |
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265 <param name="output_type" type="select" label="Output the final estimator instead?"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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266 <option value="Pipeline_Builder" selected="true">Pipeline</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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267 <option value="Final_Estimator_Builder">Final Estimator</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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268 </param> |
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269 </inputs> |
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270 <outputs> |
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271 <data format="zip" name="outfile" label="${output_type}"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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272 </outputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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273 <tests> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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274 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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275 <repeat name="pipeline_component"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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276 <conditional name="component_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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277 <param name="component_type" value="pre_processor"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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278 <conditional name="pre_processors"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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279 <param name="selected_pre_processor" value="RobustScaler"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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280 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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281 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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282 </repeat> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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283 <repeat name="pipeline_component"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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284 <conditional name="component_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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285 <param name="component_type" value="feature_selection"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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286 <conditional name="fs_algorithm_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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287 <param name="selected_algorithm" value="SelectKBest"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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288 <param name="score_func" value="f_classif"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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289 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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290 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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291 </repeat> |
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292 <param name="selected_module" value="svm"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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293 <param name="selected_estimator" value="SVR"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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294 <param name="text_params" value="kernel='linear'"/> |
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295 <output name="outfile" file="pipeline01" compare="sim_size" delta="5"/> |
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296 </test> |
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297 <test> |
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298 <conditional name="component_selector"> |
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299 <param name="component_type" value="pre_processor"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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300 <conditional name="pre_processors"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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301 <param name="selected_pre_processor" value="RobustScaler"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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302 </conditional> |
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303 </conditional> |
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304 <param name="selected_module" value="linear_model"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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305 <param name="selected_estimator" value="LassoCV"/> |
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306 <output name="outfile" file="pipeline02" compare="sim_size" delta="5"/> |
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307 </test> |
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308 <test> |
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309 <conditional name="component_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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310 <param name="component_type" value="pre_processor"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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311 <conditional name="pre_processors"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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312 <param name="selected_pre_processor" value="RobustScaler"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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313 </conditional> |
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314 </conditional> |
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315 <param name="selected_module" value="xgboost"/> |
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316 <param name="selected_estimator" value="XGBClassifier"/> |
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317 <output name="outfile" file="pipeline03" compare="sim_size" delta="5"/> |
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318 </test> |
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319 <test> |
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320 <conditional name="component_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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321 <param name="component_type" value="feature_selection"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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322 <conditional name="fs_algorithm_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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323 <param name="selected_algorithm" value="SelectFromModel"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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324 <conditional name="model_inputter"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
325 <conditional name="estimator_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
326 <param name="selected_module" value="ensemble"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
327 <param name="selected_estimator" value="AdaBoostClassifier"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
328 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
329 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
330 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
331 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
332 <section name="final_estimator"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
333 <param name="selected_module" value="svm"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
334 <param name="selected_estimator" value="LinearSVC"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
335 </section> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
336 <output name="outfile" file="pipeline04" compare="sim_size" delta="5"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
337 </test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
338 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
339 <conditional name="component_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
340 <param name="component_type" value="None"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
341 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
342 <param name="selected_module" value="ensemble"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
343 <param name="selected_estimator" value="RandomForestRegressor"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
344 <param name="text_params" value="n_estimators=100, random_state=42"/> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
345 <output name="outfile" file="pipeline05" compare="sim_size" delta="5"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
346 </test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
347 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
348 <conditional name="component_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
349 <param name="component_type" value="decomposition"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
350 <conditional name="matrix_decomposition_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
351 <param name="select_algorithm" value="PCA"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
352 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
353 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
354 <param name="selected_module" value="ensemble"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
355 <param name="selected_estimator" value="AdaBoostRegressor"/> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
356 <output name="outfile" file="pipeline06" compare="sim_size" delta="5"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
357 </test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
358 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
359 <conditional name="component_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
360 <param name="component_type" value="kernel_approximation"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
361 <conditional name="kernel_approximation_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
362 <param name="select_algorithm" value="RBFSampler"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
363 <param name="text_params" value="n_components=10, gamma=2.0"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
364 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
365 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
366 <param name="selected_module" value="ensemble"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
367 <param name="selected_estimator" value="AdaBoostClassifier"/> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
368 <output name="outfile" file="pipeline07" compare="sim_size" delta="5"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
369 </test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
370 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
371 <conditional name="component_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
372 <param name="component_type" value="FeatureAgglomeration"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
373 <conditional name="FeatureAgglomeration_selector"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
374 <param name="select_algorithm" value="FeatureAgglomeration"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
375 <param name="text_params" value="n_clusters=3, affinity='euclidean'"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
376 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
377 </conditional> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
378 <param name="selected_module" value="ensemble"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
379 <param name="selected_estimator" value="AdaBoostClassifier"/> |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
380 <output name="outfile" file="pipeline08" compare="sim_size" delta="20"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
381 </test> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
382 <test> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
383 <conditional name="component_selector"> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
384 <param name="component_type" value="skrebate"/> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
385 <conditional name="skrebate_selector"> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
386 <param name="select_algorithm" value="ReliefF"/> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
387 <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
388 </conditional> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
389 </conditional> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
390 <param name="selected_module" value="ensemble"/> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
391 <param name="selected_estimator" value="RandomForestRegressor"/> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
392 <output name="outfile" file="pipeline09" compare="sim_size" delta="5"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
393 </test> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
394 <test> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
395 <conditional name="component_selector"> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
396 <param name="component_type" value="None"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
397 </conditional> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
398 <param name="selected_module" value="ensemble"/> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
399 <param name="selected_estimator" value="AdaBoostRegressor"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
400 <output name="outfile" file="pipeline10" compare="sim_size" delta="5"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
401 </test> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
402 <test> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
403 <conditional name="component_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
404 <param name="component_type" value="imblearn"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
405 <conditional name="imblearn_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
406 <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
407 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
408 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
409 <param name="selected_module" value="ensemble"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
410 <param name="selected_estimator" value="RandomForestClassifier"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
|
411 <output name="outfile" file="pipeline11" compare="sim_size" delta="5"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
0
diff
changeset
|
412 </test> |
6
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
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diff
changeset
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413 <test expect_failure="true"> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
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diff
changeset
|
414 <conditional name="component_selector"> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
5
diff
changeset
|
415 <param name="component_type" value="None"/> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
5
diff
changeset
|
416 </conditional> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
5
diff
changeset
|
417 <param name="selected_module" value="ensemble"/> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
5
diff
changeset
|
418 <param name="selected_estimator" value="RandomForestRegressor"/> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
5
diff
changeset
|
419 <param name="text_params" value="n_estimators=__import__('os').system('ls ~')"/> |
52c4e0ef580a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents:
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diff
changeset
|
420 </test> |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
421 <test> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
422 <conditional name="component_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
|
423 <param name="component_type" value="feature_selection"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
|
424 <conditional name="fs_algorithm_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
425 <param name="selected_algorithm" value="RFE"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
426 <conditional name="estimator_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
6
diff
changeset
|
427 <param name="selected_module" value="xgboost"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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428 <param name="selected_estimator" value="XGBRegressor"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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429 <param name="text_params" value="random_state=0"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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430 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
|
431 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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432 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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433 <section name="final_estimator"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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434 <conditional name="estimator_selector"> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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435 <param name="selected_module" value="none"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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changeset
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436 </conditional> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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changeset
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437 </section> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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diff
changeset
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438 <output name="outfile" file="pipeline12" compare="sim_size" delta="5"/> |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents:
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changeset
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439 </test> |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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440 <test> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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441 <conditional name="component_selector"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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442 <param name="component_type" value="None"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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443 </conditional> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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444 <param name="selected_module" value="ensemble"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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445 <param name="selected_estimator" value="RandomForestClassifier"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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446 <param name="output_type" value="Final_Estimator_Builder"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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447 <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="5"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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448 </test> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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449 <test> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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450 <conditional name="component_selector"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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451 <param name="component_type" value="IRAPS"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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452 </conditional> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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453 <section name="final_estimator"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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454 <conditional name="estimator_selector"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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455 <param name="selected_module" value="none"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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456 </conditional> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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457 </section> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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458 <param name="output_type" value="Final_Estimator_Builder"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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459 <output name="outfile" file="pipeline14" compare="sim_size" delta="5"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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460 </test> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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461 <test> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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462 <conditional name="component_selector"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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463 <param name="component_type" value="None"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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464 </conditional> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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465 <section name="final_estimator"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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changeset
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466 <conditional name="estimator_selector"> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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467 <param name="selected_module" value="binarize_target"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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468 <param name="clf_or_regr" value="BinarizeTargetClassifier"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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469 <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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470 </conditional> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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471 </section> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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472 <param name="output_type" value="Final_Estimator_Builder"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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473 <output name="outfile" file="pipeline15" compare="sim_size" delta="5"/> |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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parents:
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changeset
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474 </test> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
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changeset
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475 </tests> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
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changeset
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476 <help> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
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changeset
|
477 <![CDATA[ |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
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478 **What it does** |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
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479 Constructs a pipeline that contains a list of transfroms and a final estimator. Pipeline assembles several steps |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
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480 that can be cross-validated together while setting different parameters. |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
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481 please refer to `Scikit-learn pipeline Pipeline`_. |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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parents:
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changeset
|
482 |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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483 **Pre-processing components** allow None, one or a combination of up to 5 transformations from `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_ and/or `skrebate`_. |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
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484 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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485 **Estimator** selector supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_ and `neighbors`_. |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
|
486 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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changeset
|
487 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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488 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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489 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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490 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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491 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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492 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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493 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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494 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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495 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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496 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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497 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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498 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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499 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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500 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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501 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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502 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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503 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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504 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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505 </help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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506 <expand macro="sklearn_citation"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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507 <expand macro="skrebate_citation"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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508 <expand macro="xgboost_citation"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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509 <expand macro="imblearn_citation"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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510 </expand> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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511 </tool> |