Mercurial > repos > bgruening > sklearn_searchcv
annotate search_model_validation.xml @ 4:2e6540c11251 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
author | bgruening |
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date | Thu, 23 Aug 2018 16:14:26 -0400 |
parents | f9fea8323bcb |
children | 0987bc3904a0 |
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91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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1 <tool id="sklearn_searchcv" name="Hyperparameter Search" version="@VERSION@"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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2 <description>using exhausitive or randomized search</description> |
91bf3f0d7455
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> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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5 </macros> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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6 <expand macro="python_requirements"> |
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f9fea8323bcb
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> |
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91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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8 </expand> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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9 <expand macro="macro_stdio"/> |
91bf3f0d7455
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> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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11 <command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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12 <![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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13 python "$sklearn_search_model_validation_script" '$inputs' |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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14 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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15 </command> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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16 <configfiles> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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17 <inputs name="inputs" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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18 <configfile name="sklearn_search_model_validation_script"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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19 <![CDATA[ |
91bf3f0d7455
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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f9fea8323bcb
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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91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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22 import json |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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23 import pandas |
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2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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24 import skrebate |
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f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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25 from sklearn import model_selection |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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26 from sklearn.exceptions import FitFailedWarning |
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91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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27 |
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2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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28 execfile("$__tool_directory__/sk_whitelist.py") |
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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29 execfile("$__tool_directory__/utils.py", globals()) |
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f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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30 |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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31 warnings.simplefilter('ignore') |
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91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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32 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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33 input_json_path = sys.argv[1] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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34 with open(input_json_path, "r") as param_handler: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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35 params = json.load(param_handler) |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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36 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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37 #handle cheatah |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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38 infile1 = "$input_options.infile1" |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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39 infile2 = "$input_options.infile2" |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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40 infile_pipeline = "$search_schemes.infile_pipeline" |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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41 outfile_result = "$outfile_result" |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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42 outfile_estimator = "$outfile_estimator" |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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43 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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44 params_builder = params['search_schemes']['search_params_builder'] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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45 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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46 input_type = params["input_options"]["selected_input"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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47 if input_type=="tabular": |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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48 header = 'infer' if params["input_options"]["header1"] else None |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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49 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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50 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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51 c = params["input_options"]["column_selector_options_1"]["col1"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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52 else: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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53 c = None |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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54 X = read_columns( |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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55 infile1, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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56 c = c, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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57 c_option = column_option, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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58 sep='\t', |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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59 header=header, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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60 parse_dates=True |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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61 ) |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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62 else: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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63 X = mmread(open("$input_options.infile1", 'r')) |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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64 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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65 header = 'infer' if params["input_options"]["header2"] else None |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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66 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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67 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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68 c = params["input_options"]["column_selector_options_2"]["col2"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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69 else: |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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70 c = None |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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71 y = read_columns( |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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72 infile2, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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73 c = c, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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74 c_option = column_option, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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75 sep='\t', |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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76 header=header, |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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77 parse_dates=True |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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78 ) |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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79 y=y.ravel() |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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80 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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81 optimizers = params["search_schemes"]["selected_search_scheme"] |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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82 optimizers = getattr(model_selection, optimizers) |
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83 |
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84 options = params["search_schemes"]["options"] |
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85 options['cv'] = get_cv( options['cv'].strip() ) |
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86 options['n_jobs'] = N_JOBS |
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87 options['scoring'] = get_scoring(options['scoring']) |
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88 if options['error_score']: |
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89 options['error_score'] = 'raise' |
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90 else: |
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91 options['error_score'] = 0 |
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92 if options['refit'] and isinstance(options['scoring'], dict): |
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93 options['refit'] = 'primary' |
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94 if 'pre_dispatch' in options and options['pre_dispatch'] == '': |
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95 options['pre_dispatch'] = None |
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96 |
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97 with open(infile_pipeline, 'rb') as pipeline_handler: |
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98 pipeline = SafePickler.load(pipeline_handler) |
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99 |
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100 search_params = get_search_params(params_builder) |
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101 searcher = optimizers(pipeline, search_params, **options) |
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102 |
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103 warnings.simplefilter('always', FitFailedWarning) |
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104 with warnings.catch_warnings(record=True) as w: |
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105 try: |
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106 searcher.fit(X, y) |
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107 except ValueError: |
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108 pass |
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109 for warning in w: |
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110 print(repr(warning.message)) |
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111 |
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112 cv_result = pandas.DataFrame(searcher.cv_results_) |
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113 cv_result.to_csv(path_or_buf=outfile_result, sep='\t', header=True, index=False) |
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114 |
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115 #if $save: |
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116 with open(outfile_estimator, "wb") as output_handler: |
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117 pickle.dump(searcher.best_estimator_, output_handler, pickle.HIGHEST_PROTOCOL) |
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118 #end if |
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119 |
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120 ]]> |
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121 </configfile> |
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122 </configfiles> |
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123 <inputs> |
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124 <conditional name="search_schemes"> |
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125 <param name="selected_search_scheme" type="select" label="Select a model selection search scheme:"> |
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126 <option value="GridSearchCV" selected="true">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option> |
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127 <option value="RandomizedSearchCV">RandomizedSearchCV - Randomized search on hyper parameters for an estimator</option> |
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128 </param> |
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129 <when value="GridSearchCV"> |
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130 <expand macro="search_cv_estimator"/> |
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131 <section name="options" title="Advanced Options for SearchCV" expanded="false"> |
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132 <expand macro="search_cv_options"/> |
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133 </section> |
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134 </when> |
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135 <when value="RandomizedSearchCV"> |
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136 <expand macro="search_cv_estimator"/> |
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137 <section name="options" title="Advanced Options for SearchCV" expanded="false"> |
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138 <expand macro="search_cv_options"/> |
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139 <param argument="n_iter" type="integer" value="10" label="Number of parameter settings that are sampled"/> |
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140 <expand macro="random_state"/> |
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141 </section> |
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142 </when> |
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143 </conditional> |
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144 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Save the best estimator/pipeline?"/> |
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145 <expand macro="sl_mixed_input"/> |
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146 </inputs> |
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147 <outputs> |
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148 <data format="tabular" name="outfile_result"/> |
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149 <data format="zip" name="outfile_estimator"> |
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150 <filter>save</filter> |
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151 </data> |
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152 </outputs> |
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153 <tests> |
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154 <test> |
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155 <param name="selected_search_scheme" value="GridSearchCV"/> |
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156 <param name="infile_pipeline" value="pipeline01" ftype="zip"/> |
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157 <conditional name="search_param_selector"> |
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158 <param name="search_p" value="C: [1, 10, 100, 1000]"/> |
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159 <param name="selected_param_type" value="final_estimator_p"/> |
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160 </conditional> |
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161 <conditional name="search_param_selector"> |
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162 <param name="search_p" value="k: [-1, 3, 5, 7, 9]"/> |
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163 <param name="selected_param_type" value="prep_2_p"/> |
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164 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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165 <param name="error_score" value="false"/> |
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166 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
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167 <param name="header1" value="true" /> |
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168 <param name="selected_column_selector_option" value="all_columns"/> |
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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="infile2" value="regression_y.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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170 <param name="header2" value="true" /> |
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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_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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172 <output name="outfile_result" > |
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173 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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174 <has_text_matching expression="[^/d]+0.7938837807353147[^/d]+{u'estimator__C': 1, u'preprocessing_2__k': 9}[^/d]+1" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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175 <has_text text="0.0"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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176 </assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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177 </output> |
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178 </test> |
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179 <test> |
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180 <param name="selected_search_scheme" value="RandomizedSearchCV"/> |
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181 <param name="infile_pipeline" value="pipeline01" ftype="zip"/> |
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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="search_param_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="search_p" value="C: [1, 10, 100, 1000]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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184 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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185 </conditional> |
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186 <conditional name="search_param_selector"> |
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187 <param name="search_p" value="kernel: ['linear', 'poly', 'rbf', 'sigmoid']"/> |
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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_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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189 </conditional> |
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190 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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191 <param name="search_p" value="k: [3, 5, 7, 9]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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192 <param name="selected_param_type" value="prep_2_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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193 </conditional> |
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194 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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195 <param name="search_p" value="with_centering: [True, False]"/> |
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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_param_type" value="prep_1_p"/> |
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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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198 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
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199 <param name="header1" value="true" /> |
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200 <param name="selected_column_selector_option" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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201 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
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202 <param name="header2" value="true" /> |
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203 <param name="selected_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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204 <output name="outfile_result" > |
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205 <assert_contents> |
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206 <has_n_columns n="15" /> |
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207 <has_text text="param_preprocessing_1__with_centering"/> |
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208 </assert_contents> |
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209 </output> |
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210 </test> |
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211 <test> |
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212 <param name="selected_search_scheme" value="RandomizedSearchCV"/> |
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213 <param name="infile_pipeline" value="pipeline03" ftype="zip"/> |
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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 name="search_param_selector"> |
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215 <param name="search_p" value="n_estimators: np_arange(50, 1001, 50)"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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216 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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217 </conditional> |
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218 <conditional name="search_param_selector"> |
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219 <param name="search_p" value="max_depth: scipy_stats_randint(1, 51)"/> |
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220 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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221 </conditional> |
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222 <conditional name="search_param_selector"> |
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223 <param name="search_p" value="gamma: scipy_stats_uniform(0., 1.)"/> |
0
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224 <param name="selected_param_type" value="final_estimator_p"/> |
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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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226 <conditional name="search_param_selector"> |
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227 <param name="search_p" value="random_state: [324089]"/> |
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228 <param name="selected_param_type" value="final_estimator_p"/> |
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229 </conditional> |
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230 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
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231 <param name="header1" value="true" /> |
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232 <param name="selected_column_selector_option" value="all_columns"/> |
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233 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
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234 <param name="header2" value="true" /> |
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235 <param name="selected_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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236 <output name="outfile_result" > |
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237 <assert_contents> |
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238 <has_n_columns n="15" /> |
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239 <has_text text="param_estimator__max_depth"/> |
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240 </assert_contents> |
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241 </output> |
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242 </test> |
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243 <test> |
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244 <param name="selected_search_scheme" value="GridSearchCV"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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245 <param name="infile_pipeline" value="pipeline04" ftype="zip"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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246 <conditional name="search_param_selector"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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247 <param name="search_p" value="random_state: list(range(100, 1001, 100))"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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248 <param name="selected_param_type" value="final_estimator_p"/> |
91bf3f0d7455
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 <conditional name="search_param_selector"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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251 <param name="search_p" value="estimator: [ensemble_ExtraTreesClassifier(n_estimators=100, random_state=324089)]"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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252 <param name="selected_param_type" value="prep_1_p"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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253 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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254 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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255 <param name="header1" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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256 <param name="selected_column_selector_option" value="all_columns"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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257 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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258 <param name="header2" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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259 <param name="selected_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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260 <output name="outfile_result"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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261 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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262 <has_n_columns n="13"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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263 <has_text text="0.05363984674329502"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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264 </assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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265 </output> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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266 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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267 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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268 <param name="selected_search_scheme" value="GridSearchCV"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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269 <param name="infile_pipeline" value="pipeline01" ftype="zip"/> |
0
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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270 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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271 <param name="search_p" value="C: [1, 10, 100, 1000]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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272 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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273 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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274 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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275 <param name="header1" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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276 <param name="selected_column_selector_option" value="all_columns"/> |
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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="infile2" value="regression_y.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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278 <param name="header2" value="true" /> |
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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_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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280 <output name="outfile_estimator" file="searchCV01" 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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281 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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282 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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283 <param name="selected_search_scheme" value="GridSearchCV"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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284 <param name="infile_pipeline" value="pipeline06" ftype="zip"/> |
0
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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285 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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286 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/> |
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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_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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288 </conditional> |
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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 name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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290 <param name="search_p" value="random_state: [324089]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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291 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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292 </conditional> |
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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="infile1" value="regression_X.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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294 <param name="header1" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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295 <param name="selected_column_selector_option" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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296 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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297 <param name="header2" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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298 <param name="selected_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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299 <output name="outfile_result"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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300 <assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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301 <has_n_columns n="13"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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302 <has_text_matching expression=".+0.7772355090078996[^/w]+1000[^/d]" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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303 </assert_contents> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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304 </output> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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305 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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306 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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307 <param name="selected_search_scheme" value="GridSearchCV"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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308 <param name="infile_pipeline" value="pipeline07" ftype="zip"/> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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309 <conditional name="search_param_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="search_p" value="n_estimators: [10, 50, 100, 200]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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311 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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312 </conditional> |
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313 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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314 <param name="search_p" value="random_state: [324089]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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315 <param name="selected_param_type" value="final_estimator_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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316 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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317 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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318 <param name="search_p" value="gamma: [1.0, 2.0]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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319 <param name="selected_param_type" value="prep_1_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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320 </conditional> |
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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="infile1" value="regression_X.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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322 <param name="header1" value="true" /> |
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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_column_selector_option" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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|
324 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
325 <param name="header2" value="true" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
326 <param name="selected_column_selector_option2" value="all_columns"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
327 <output name="outfile_result"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
328 <assert_contents> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
329 <has_n_columns n="14"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
330 <has_text_matching expression=".+0.05747126436781609[^/d]" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
331 </assert_contents> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
332 </output> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
333 </test> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
334 <test> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
335 <param name="selected_search_scheme" value="GridSearchCV"/> |
4
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
3
diff
changeset
|
336 <param name="infile_pipeline" value="pipeline08" ftype="zip"/> |
0
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
337 <conditional name="search_param_selector"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
338 <param name="search_p" value="n_estimators: [10, 50, 100, 200]"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
339 <param name="selected_param_type" value="final_estimator_p"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
340 </conditional> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
341 <conditional name="search_param_selector"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
342 <param name="search_p" value="random_state: [324089]"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
343 <param name="selected_param_type" value="final_estimator_p"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
344 </conditional> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
345 <conditional name="search_param_selector"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
346 <param name="search_p" value="linkage: ['ward', 'complete', 'average']"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
347 <param name="selected_param_type" value="prep_1_p"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
348 </conditional> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
349 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
350 <param name="header1" value="true" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
351 <param name="selected_column_selector_option" value="all_columns"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
352 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
353 <param name="header2" value="true" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
354 <param name="selected_column_selector_option2" value="all_columns"/> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
355 <output name="outfile_result"> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
356 <assert_contents> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
357 <has_text_matching expression=".+0.08045977011494253[^/w]+10[^/w]" /> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
358 </assert_contents> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
359 </output> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
diff
changeset
|
360 </test> |
2
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
361 <test> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
362 <param name="selected_search_scheme" value="GridSearchCV"/> |
4
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
3
diff
changeset
|
363 <param name="infile_pipeline" value="pipeline01" ftype="zip"/> |
2
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
364 <conditional name="search_param_selector"> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
365 <param name="search_p" value="C: [1, 10, 100, 1000]"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
366 <param name="selected_param_type" value="final_estimator_p"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
367 </conditional> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
368 <param name='cv' value="StratifiedKFold(n_splits=3, shuffle=True, random_state=10)"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
369 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
370 <param name="header1" value="true" /> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
371 <param name="selected_column_selector_option" value="all_columns"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
372 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
373 <param name="header2" value="true" /> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
374 <param name="selected_column_selector_option2" value="all_columns"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
375 <output name="outfile_estimator" file="searchCV01" compare="sim_size" delta="1"/> |
907bb0418c9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit b1e5fa3170484d2cc3396f2abe99bb8cfcfa9c65
bgruening
parents:
0
diff
changeset
|
376 </test> |
3
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
377 <test> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
378 <param name="selected_search_scheme" value="GridSearchCV"/> |
4
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
3
diff
changeset
|
379 <param name="infile_pipeline" value="pipeline03" ftype="zip"/> |
3
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
380 <conditional name="search_param_selector"> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
381 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
382 <param name="selected_param_type" value="final_estimator_p"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
383 </conditional> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
384 <conditional name="search_param_selector"> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
385 <param name="search_p" value="random_state: [324089]"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
386 <param name="selected_param_type" value="final_estimator_p"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
387 </conditional> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
388 <param name="primary_scoring" value="balanced_accuracy"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
389 <param name="cv" value="StratifiedKFold(n_splits=3, shuffle=True, random_state=10)"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
390 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
391 <param name="header1" value="true" /> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
392 <param name="selected_column_selector_option" value="all_columns"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
393 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
394 <param name="header2" value="true" /> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
395 <param name="selected_column_selector_option2" value="all_columns"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
396 <output name="outfile_result" > |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
397 <assert_contents> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
398 <has_n_columns n="13" /> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
399 <has_text text="0.05366527890058046"/> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
400 </assert_contents> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
401 </output> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
changeset
|
402 </test> |
f9fea8323bcb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
2
diff
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|
403 <test> |
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404 <param name="selected_search_scheme" value="GridSearchCV"/> |
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405 <param name="infile_pipeline" value="pipeline09" ftype="zip"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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406 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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407 <param name="search_p" value="n_neighbors: [50, 100, 150, 200]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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408 <param name="selected_param_type" value="prep_1_p"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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409 </conditional> |
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410 <conditional name="search_param_selector"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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411 <param name="search_p" value="random_state: [324089]"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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412 <param name="selected_param_type" value="final_estimator_p"/> |
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413 </conditional> |
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414 <param name="primary_scoring" value="explained_variance"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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415 <param name="secondary_scoring" value="neg_mean_squared_error,r2"/> |
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416 <param name="cv" value="StratifiedKFold(n_splits=3, shuffle=True, random_state=10)"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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417 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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418 <param name="header1" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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419 <param name="selected_column_selector_option" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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420 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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421 <param name="header2" value="true" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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422 <param name="selected_column_selector_option2" value="all_columns"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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423 <output name="outfile_result" > |
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424 <assert_contents> |
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425 <has_n_columns n="25" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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426 <has_text text="0.7881203921915186"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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427 <has_text text="0.7880692034558879"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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428 <has_text text="-29.381892762877825"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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429 </assert_contents> |
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430 </output> |
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431 </test> |
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432 </tests> |
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433 <help> |
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434 <![CDATA[ |
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435 **What it does** |
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436 Searches optimized parameter values for an estimator or pipeline through either exhaustive grid cross validation search or Randomized cross validation search. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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437 please refer to `Scikit-learn model_selection GridSearchCV`_, `Scikit-learn model_selection RandomizedSearchCV`_ and `Tuning hyper-parameters`_. |
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438 |
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439 **How to choose search patameters?** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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440 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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441 Please refer to `svm`_, `linear_model`_, `ensemble`_, `naive_bayes`_, `tree`_, `neighbors`_ and `xgboost`_ for estimator parameters. |
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442 Refer to `sklearn.preprocessing`_, `feature_selection`_, `decomposition`_, `kernel_approximation`_, `cluster.FeatureAgglomeration`_ and `skrebate`_ for parameter in the pre-processing steps. |
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443 |
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444 **Search parameter input** accepts parameter and setting in key:value pair. One pair per input box. Setting can be list, numpy array, or distribution. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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445 The evaluation of settings supports operations in Math, list comprehension, numpy.arange(np_arange), most numpy.random(e.g., np_random_uniform) and some scipy.stats(e.g., scipy_stats_zipf) classes or functions, and others. |
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446 |
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447 **Examples:** |
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448 |
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449 - K: [3, 5, 7, 9] |
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450 |
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451 - n_estimators: list(range(50, 1001, 50)) |
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452 |
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453 - gamma: np_arange(0.01, 1, 0.1) |
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454 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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455 - alpha: np_random_choice(list(range(1, 51)) + [None], size=20) |
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456 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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457 - max_depth: scipy_stats_randin(1, 11) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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458 |
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459 - estimator: [ensemble_ExtraTreesClassifier(n_estimators=100, random_state=324089)] |
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460 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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461 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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462 .. _`Scikit-learn model_selection GridSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.GridSearchCV.html |
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463 .. _`Scikit-learn model_selection RandomizedSearchCV`: http://scikit-learn.org/stable/modules/generated/sklearn.model_selection.RandomizedSearchCV.html |
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464 .. _`Tuning hyper-parameters`: http://scikit-learn.org/stable/modules/grid_search.html |
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465 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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466 .. _`svm`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.svm |
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467 .. _`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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468 .. _`ensemble`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.ensemble |
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469 .. _`naive_bayes`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.naive_bayes |
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470 .. _`tree`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.tree |
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471 .. _`neighbors`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.neighbors |
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472 .. _`xgboost`: https://xgboost.readthedocs.io/en/latest/python/python_api.html |
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473 |
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474 .. _`sklearn.preprocessing`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.preprocessing |
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475 .. _`feature_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.feature_selection |
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476 .. _`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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477 .. _`kernel_approximation`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.kernel_approximation |
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478 .. _`cluster.FeatureAgglomeration`: http://scikit-learn.org/stable/modules/generated/sklearn.cluster.FeatureAgglomeration.html |
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479 .. _`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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480 |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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481 ]]> |
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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482 </help> |
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2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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483 <expand macro="sklearn_citation"> |
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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484 <expand macro="skrebate_citation"/> |
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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485 <expand macro="xgboost_citation"/> |
2e6540c11251
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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486 </expand> |
0
91bf3f0d7455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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487 </tool> |