Mercurial > repos > bgruening > sklearn_build_pipeline
annotate pipeline.xml @ 3:0857964e07c2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
author | bgruening |
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date | Fri, 17 Aug 2018 12:26:40 -0400 |
parents | 73535ddcfa69 |
children | 86450dde8682 |
rev | line source |
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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> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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6 <expand macro="python_requirements"> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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7 <requirement type="package" version="0.6">skrebate</requirement> |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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8 </expand> |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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9 <expand macro="macro_stdio"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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10 <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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11 <command> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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12 <![CDATA[ |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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13 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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14 ]]> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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15 </command> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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16 <configfiles> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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17 <inputs name="inputs" /> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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18 <configfile name="sklearn_pipeline_script"> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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19 <![CDATA[ |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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20 import sys |
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0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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21 import os |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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22 import json |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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23 import pickle |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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24 import pprint |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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25 import skrebate |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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26 from sklearn import (preprocessing, svm, linear_model, ensemble, naive_bayes, |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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27 tree, neighbors, decomposition, kernel_approximation, cluster) |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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28 from sklearn.pipeline import Pipeline |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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29 |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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30 execfile("$__tool_directory__/utils.py") |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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31 |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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32 safe_eval = SafeEval() |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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33 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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34 input_json_path = sys.argv[1] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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35 with open(input_json_path, "r") as param_handler: |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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36 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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37 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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38 pipeline_steps = [] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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39 |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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40 def get_component(input_json, check_none=False): |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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41 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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42 if not check_none: |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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43 return |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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44 else: |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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45 sys.exit("The pre-processing component type can't be None when the number of components is greater than 1.") |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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46 if input_json['component_type'] == 'pre_processor': |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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47 preprocessor = input_json["pre_processors"]["selected_pre_processor"] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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48 pre_processor_options = input_json["pre_processors"]["options"] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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49 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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50 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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51 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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52 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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53 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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54 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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55 obj = getattr(decomposition, algorithm)() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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56 options = input_json['matrix_decomposition_selector']['text_params'].strip() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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57 if options != "": |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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58 options = safe_eval('dict(' + options + ')') |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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59 obj.set_params(**options) |
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0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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60 elif input_json['component_type'] == 'kernel_approximation': |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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61 algorithm = input_json['kernel_approximation_selector']['select_algorithm'] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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62 obj = getattr(kernel_approximation, algorithm)() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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63 options = input_json['kernel_approximation_selector']['text_params'].strip() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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64 if options != "": |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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65 options = safe_eval('dict(' + options + ')') |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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66 obj.set_params(**options) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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67 elif input_json['component_type'] == 'FeatureAgglomeration': |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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68 algorithm = input_json['FeatureAgglomeration_selector']['select_algorithm'] |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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69 obj = getattr(cluster, algorithm)() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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70 options = input_json['FeatureAgglomeration_selector']['text_params'].strip() |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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71 if options != "": |
3
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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72 options = safe_eval('dict(' + options + ')') |
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73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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73 obj.set_params(**options) |
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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'] == 'skrebate': |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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75 algorithm = input_json['skrebate_selector']['select_algorithm'] |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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76 if algorithm == 'TuRF': |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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77 obj = getattr(skrebate, algorithm)(core_algorithm='ReliefF') |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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78 else: |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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79 obj = getattr(skrebate, algorithm)() |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
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80 options = input_json['skrebate_selector']['text_params'].strip() |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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81 if options != "": |
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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82 options = safe_eval('dict(' + options + ')') |
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83 obj.set_params(**options) |
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84 if 'n_jobs' in obj.get_params(): |
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85 obj.set_params( n_jobs=N_JOBS ) |
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86 return obj |
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87 |
0
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88 if len(params['pipeline_component']) == 1: |
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89 step_obj = get_component( params['pipeline_component'][0]['component_selector']) |
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90 if step_obj: |
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91 pipeline_steps.append( ('preprocessing_1', step_obj) ) |
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92 else: |
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93 for i, c in enumerate(params['pipeline_component']): |
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94 step_obj = get_component( c['component_selector'], check_none=True ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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95 pipeline_steps.append( ('preprocessing_' + str(i+1), step_obj) ) |
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96 |
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97 # Set up final estimator and add to pipeline. |
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98 estimator_json = params["final_estimator"]['estimator_selector'] |
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99 estimator = get_estimator(estimator_json) |
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100 |
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101 pipeline_steps.append( ('estimator', estimator) ) |
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102 |
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103 pipeline = Pipeline(pipeline_steps) |
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104 pprint.pprint(pipeline.named_steps) |
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105 |
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106 with open("$outfile", 'wb') as out_handler: |
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107 pickle.dump(pipeline, out_handler, pickle.HIGHEST_PROTOCOL) |
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108 |
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109 ]]> |
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110 </configfile> |
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111 </configfiles> |
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112 <inputs> |
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113 <repeat name="pipeline_component" min="1" max="5" title="Pre-processing step"> |
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114 <conditional name="component_selector"> |
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115 <param name="component_type" type="select" label="Choose the type of transformation:"> |
3
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116 <option value="None" selected="true">None</option> |
0
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117 <option value="pre_processor">Sklearn Preprocessor</option> |
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118 <option value="feature_selection">Feature Selection</option> |
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119 <option value="decomposition">Matrix Decomposition</option> |
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120 <option value="kernel_approximation">Kernel Approximation</option> |
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121 <option value="FeatureAgglomeration">Agglomerate Features</option> |
3
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122 <option value="skrebate">Skrebate algorithm</option> |
0
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123 </param> |
3
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124 <when value="None"/> |
0
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125 <when value="pre_processor"> |
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126 <conditional name="pre_processors"> |
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127 <expand macro="sparse_preprocessors_ext" /> |
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128 <expand macro="sparse_preprocessor_options_ext" /> |
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129 </conditional> |
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130 </when> |
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131 <when value="feature_selection"> |
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132 <expand macro="feature_selection_all"> |
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133 <expand macro="fs_selectfrommodel_no_prefitted"/> |
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134 </expand> |
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135 </when> |
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136 <when value="decomposition"> |
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137 <expand macro="matrix_decomposition_all"/> |
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138 </when> |
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139 <when value="kernel_approximation"> |
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140 <expand macro="kernel_approximation_all"/> |
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141 </when> |
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142 <when value="FeatureAgglomeration"> |
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143 <expand macro="FeatureAgglomeration"/> |
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144 </when> |
3
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145 <when value="skrebate"> |
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146 <expand macro="skrebate"/> |
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147 </when> |
0
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148 </conditional> |
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149 </repeat> |
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150 <section name="final_estimator" title="Final Estimator" expanded="true"> |
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151 <expand macro="estimator_selector_all" /> |
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152 </section> |
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153 </inputs> |
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154 <outputs> |
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155 <data format="zip" name="outfile"/> |
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156 </outputs> |
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157 <tests> |
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158 <test> |
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159 <repeat name="pipeline_component"> |
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160 <conditional name="component_selector"> |
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161 <param name="component_type" value="pre_processor"/> |
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162 <conditional name="pre_processors"> |
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163 <param name="selected_pre_processor" value="RobustScaler"/> |
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164 </conditional> |
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165 </conditional> |
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166 </repeat> |
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167 <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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168 <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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169 <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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170 <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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171 <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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172 <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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173 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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174 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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|
175 </repeat> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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|
176 <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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177 <param name="selected_estimator" value="SVR"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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0
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178 <param name="text_params" value="kernel='linear'"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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179 <output name="outfile" file="pipeline01" compare="sim_size" delta="1"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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180 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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181 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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182 <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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183 <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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184 <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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185 <param name="selected_pre_processor" value="RobustScaler"/> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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186 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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187 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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188 <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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189 <param name="selected_estimator" value="LassoCV"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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190 <output name="outfile" file="pipeline02" compare="sim_size" delta="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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191 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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192 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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193 <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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194 <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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195 <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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196 <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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197 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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198 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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199 <param name="selected_module" value="xgboost"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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200 <param name="selected_estimator" value="XGBClassifier"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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201 <output name="outfile" file="pipeline03" compare="sim_size" delta="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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202 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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203 <test> |
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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204 <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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205 <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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changeset
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206 <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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207 <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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208 <conditional name="model_inputter"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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209 <conditional name="estimator_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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210 <param name="selected_module" value="ensemble"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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211 <param name="selected_estimator" value="AdaBoostClassifier"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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|
212 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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213 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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214 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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215 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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216 <section name="final_estimator"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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217 <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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218 <param name="selected_estimator" value="LinearSVC"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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219 </section> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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220 <output name="outfile" file="pipeline04" compare="sim_size" delta="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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221 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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222 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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223 <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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224 <param name="component_type" value="None"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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225 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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226 <param name="selected_module" value="ensemble"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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227 <param name="selected_estimator" value="RandomForestRegressor"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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228 <param name="text_params" value="n_estimators=100, random_state=42"/> |
0
73535ddcfa69
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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229 <output name="outfile" file="pipeline05" compare="sim_size" delta="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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230 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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231 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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232 <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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233 <param name="component_type" value="decomposition"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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234 <conditional name="matrix_decomposition_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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235 <param name="select_algorithm" value="PCA"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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236 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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237 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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238 <param name="selected_module" value="ensemble"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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239 <param name="selected_estimator" value="AdaBoostRegressor"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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240 <output name="outfile" file="pipeline06" compare="sim_size" delta="1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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241 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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242 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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243 <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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244 <param name="component_type" value="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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245 <conditional name="kernel_approximation_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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246 <param name="select_algorithm" value="RBFSampler"/> |
3
0857964e07c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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0
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247 <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
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248 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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249 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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250 <param name="selected_module" value="ensemble"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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251 <param name="selected_estimator" value="AdaBoostClassifier"/> |
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252 <output name="outfile" file="pipeline07" compare="sim_size" delta="1"/> |
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253 </test> |
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254 <test> |
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255 <conditional name="component_selector"> |
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256 <param name="component_type" value="FeatureAgglomeration"/> |
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257 <conditional name="FeatureAgglomeration_selector"> |
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258 <param name="select_algorithm" value="FeatureAgglomeration"/> |
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259 <param name="text_params" value="n_clusters=3, affinity='euclidean'"/> |
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260 </conditional> |
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261 </conditional> |
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262 <param name="selected_module" value="ensemble"/> |
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263 <param name="selected_estimator" value="AdaBoostClassifier"/> |
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264 <output name="outfile" file="pipeline08" compare="sim_size" delta="1"/> |
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265 </test> |
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266 <test> |
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267 <conditional name="component_selector"> |
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268 <param name="component_type" value="skrebate"/> |
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269 <conditional name="skrebate_selector"> |
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270 <param name="select_algorithm" value="ReliefF"/> |
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271 <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/> |
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272 </conditional> |
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273 </conditional> |
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274 <param name="selected_module" value="ensemble"/> |
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275 <param name="selected_estimator" value="RandomForestRegressor"/> |
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276 <output name="outfile" file="pipeline09" compare="sim_size" delta="1"/> |
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277 </test> |
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278 <test> |
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279 <conditional name="component_selector"> |
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280 <param name="component_type" value="skrebate"/> |
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281 <conditional name="skrebate_selector"> |
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282 <param name="select_algorithm" value="TuRF"/> |
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283 <param name="text_params" value=""/> |
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284 </conditional> |
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285 </conditional> |
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286 <param name="selected_module" value="ensemble"/> |
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287 <param name="selected_estimator" value="RandomForestRegressor"/> |
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288 <output name="outfile" file="pipeline10" compare="sim_size" delta="1"/> |
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289 </test> |
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290 </tests> |
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291 <help> |
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292 <![CDATA[ |
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293 **What it does** |
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294 Constructs a pipeline that contains a list of transfroms and a final estimator. Pipeline assembles several steps |
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295 that can be cross-validated together while setting different parameters. |
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296 please refer to `Scikit-learn pipeline Pipeline`_. |
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297 |
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298 **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`_. |
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299 |
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300 **Estimator** selector supports estimators from `xgboost`_ and many scikit-learn modules, including `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_ and `neighbors`_. |
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301 |
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302 |
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303 .. _`Scikit-learn pipeline Pipeline`: http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.html |
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304 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm |
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305 .. _`linear_model`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.linear_model |
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306 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble |
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307 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes |
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308 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree |
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309 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors |
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310 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html |
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311 |
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312 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing |
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313 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection |
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314 .. _`decomposition`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.decomposition |
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315 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation |
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316 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html |
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317 .. _`skrebate`: https://epistasislab.github.io/scikit-rebate/using/ |
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318 |
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319 ]]> |
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320 </help> |
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321 <expand macro="sklearn_citation"/> |
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322 </tool> |