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annotate main_macros.xml @ 12:a31759a19a09 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
author bgruening
date Tue, 05 Jun 2018 06:41:31 -0400
parents d8fa28fb18f8
children 14f66545cc73
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12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
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diff changeset
1 <macros>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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2 <token name="@VERSION@">0.9</token>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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3
1
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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4 <token name="@COLUMNS_FUNCTION@">
12
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
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5 def read_columns(f, c=None, c_option='by_index_number', return_df=False, **args):
4
fb95a61a0a89 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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6 data = pandas.read_csv(f, **args)
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a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
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7 if c_option == 'by_index_number':
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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8 cols = list(map(lambda x: x - 1, c))
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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9 data = data.iloc[:,cols]
10
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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10 y = data.values
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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11 if return_df:
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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12 return y, data
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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13 else:
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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14 return y
1
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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15 return y
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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16 </token>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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17
11
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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18 ## generate an instance for one of sklearn.feature_selection classes
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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19 <token name="@FEATURE_SELECTOR_FUNCTION@">
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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20 def feature_selector(inputs):
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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21 selector = inputs["selected_algorithm"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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22 selector = getattr(sklearn.feature_selection, selector)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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23 options = inputs["options"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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24
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25 if inputs['selected_algorithm'] == 'SelectFromModel':
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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26 if not options['threshold'] or options['threshold'] == 'None':
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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27 options['threshold'] = None
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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28 if 'extra_estimator' in inputs and inputs['extra_estimator']['has_estimator'] == 'no_load':
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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29 fitted_estimator = pickle.load(open("inputs['extra_estimator']['fitted_estimator']", 'r'))
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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30 new_selector = selector(fitted_estimator, prefit=True, **options)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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31 else:
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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32 estimator=inputs["estimator"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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33 if inputs["extra_estimator"]["has_estimator"]=='no':
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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34 estimator=inputs["extra_estimator"]["new_estimator"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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35 estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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36 new_selector = selector(estimator, **options)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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37
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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38 elif inputs['selected_algorithm'] in ['RFE', 'RFECV']:
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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39 if 'scoring' in options and (not options['scoring'] or options['scoring'] == 'None'):
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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40 options['scoring'] = None
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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41 estimator=inputs["estimator"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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42 if inputs["extra_estimator"]["has_estimator"]=='no':
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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43 estimator=inputs["extra_estimator"]["new_estimator"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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44 estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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45 new_selector = selector(estimator, **options)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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46
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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47 elif inputs['selected_algorithm'] == "VarianceThreshold":
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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48 new_selector = selector(**options)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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49
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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50 else:
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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51 score_func = inputs["score_func"]
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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52 score_func = getattr(sklearn.feature_selection, score_func)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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53 new_selector = selector(score_func, **options)
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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54
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55 return new_selector
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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56 </token>
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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57
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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58 <xml name="python_requirements">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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59 <requirements>
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60 <requirement type="package" version="2.7">python</requirement>
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61 <requirement type="package" version="0.19.1">scikit-learn</requirement>
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62 <requirement type="package" version="0.22.0">pandas</requirement>
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63 <yield />
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64 </requirements>
0
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65 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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66
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67 <xml name="macro_stdio">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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68 <stdio>
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69 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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70 </stdio>
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71 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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72
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73
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74 <!--Generic interface-->
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75 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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76 <conditional name="selected_tasks">
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77 <param name="selected_task" type="select" label="Select a Classification Task">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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78 <option value="train" selected="true">Train a model</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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79 <option value="load">Load a model and predict</option>
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80 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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81 <when value="load">
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82 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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83 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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84 <conditional name="prediction_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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85 <param name="prediction_option" type="select" label="Select the type of prediction">
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86 <option value="predict">Predict class labels</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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87 <option value="advanced">Include advanced options</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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88 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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89 <when value="predict">
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90 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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91 <when value="advanced">
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92 </when>
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93 </conditional>
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94 </when>
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95 <when value="train">
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96 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
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97 <conditional name="selected_algorithms">
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98 <yield />
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99 </conditional>
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100 </when>
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101 </conditional>
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102 </xml>
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103
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104 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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105 <conditional name="selected_tasks">
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106 <param name="selected_task" type="select" label="Select a Classification Task">
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107 <option value="train" selected="true">Train a model</option>
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108 <option value="load">Load a model and predict</option>
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109 </param>
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110 <when value="load">
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111 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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112 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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113 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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114 <conditional name="prediction_options">
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115 <param name="prediction_option" type="select" label="Select the type of prediction">
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116 <option value="predict">Predict class labels</option>
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117 <option value="advanced">Include advanced options</option>
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118 </param>
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119 <when value="predict">
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120 </when>
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121 <when value="advanced">
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122 </when>
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123 </conditional>
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124 </when>
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125 <when value="train">
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126 <conditional name="selected_algorithms">
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127 <yield />
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128 </conditional>
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129 </when>
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130 </conditional>
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131 </xml>
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132
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133 <xml name="advanced_section">
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134 <section name="options" title="Advanced Options" expanded="False">
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135 <yield />
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136 </section>
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137 </xml>
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138
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139
2
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140 <!--Generalized Linear Models-->
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141 <xml name="loss" token_help=" " token_select="false">
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142 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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143 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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144 <option value="huber">huber</option>
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145 <option value="epsilon_insensitive">epsilon insensitive</option>
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146 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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147 <yield/>
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148 </param>
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149 </xml>
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150
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151 <xml name="penalty" token_help=" ">
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152 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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153 <option value="l2" selected="true">l2</option>
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154 <option value="l1">l1</option>
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155 <option value="elasticnet">elastic net</option>
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156 <option value="none">none</option>
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157 <yield/>
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158 </param>
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159 </xml>
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160
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161 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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162 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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163 </xml>
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164
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165 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. ">
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166 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
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167 </xml>
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168
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169 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
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170 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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171 <option value="optimal" selected="@SELECTED1@">optimal</option>
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172 <option value="constant">constant</option>
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173 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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174 <yield/>
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175 </param>
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176 </xml>
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177
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178 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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179 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
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180 </xml>
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181
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182 <xml name="power_t" token_default_value="0.5" token_help=" ">
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183 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
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184 </xml>
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185
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186 <xml name="normalize" token_checked="false" token_help=" ">
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187 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
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188 </xml>
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189
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190 <xml name="copy_X" token_checked="true" token_help=" ">
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191 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. "/>
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192 </xml>
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193
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194 <xml name="ridge_params">
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195 <expand macro="normalize"/>
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196 <expand macro="alpha" default_value="1.0"/>
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197 <expand macro="fit_intercept"/>
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198 <expand macro="max_iter" default_value=""/>
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199 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
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200 <!--class_weight-->
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201 <expand macro="copy_X"/>
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202 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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203 <option value="auto" selected="true">auto</option>
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204 <option value="svd">svd</option>
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205 <option value="cholesky">cholesky</option>
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206 <option value="lsqr">lsqr</option>
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207 <option value="sparse_cg">sparse_cg</option>
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208 <option value="sag">sag</option>
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209 </param>
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210 <expand macro="random_state"/>
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211 </xml>
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212
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213 <!--Ensemble methods-->
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214 <xml name="n_estimators" token_default_value="10" token_help=" ">
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215 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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216 </xml>
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217
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218 <xml name="max_depth" token_default_value="" token_help=" ">
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219 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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220 </xml>
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221
7
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222 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
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223 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
0
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224 </xml>
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225
7
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226 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
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227 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
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228 </xml>
2
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229
0
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230 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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231 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/>
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232 </xml>
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233
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234 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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235 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
2
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236 </xml>
0
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237
7
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238 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
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239 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/>
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240 </xml>
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241
0
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242 <xml name="bootstrap" token_checked="true" token_help=" ">
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243 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/>
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244 </xml>
0
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245
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246 <xml name="criterion" token_help=" ">
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247 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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248 <option value="gini" selected="true">Gini impurity</option>
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249 <option value="entropy">Information gain</option>
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250 <yield/>
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251 </param>
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252 </xml>
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253
7
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254 <xml name="criterion2" token_help="">
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255 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
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256 <option value="mse">mse - mean squared error</option>
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257 <option value="mae">mae - mean absolute error</option>
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258 <yield/>
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259 </param>
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260 </xml>
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261
2
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262 <xml name="oob_score" token_checked="false" token_help=" ">
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263 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
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264 </xml>
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265
7
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266 <xml name="max_features">
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267 <conditional name="select_max_features">
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268 <param argument="max_features" type="select" label="max_features">
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269 <option value="auto" selected="true">auto - max_features=n_features</option>
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270 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
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271 <option value="log2">log2 - max_features=log2(n_features)</option>
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272 <option value="number_input">I want to type the number in or input None type</option>
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273 </param>
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274 <when value="auto">
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275 </when>
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276 <when value="sqrt">
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277 </when>
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278 <when value="log2">
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279 </when>
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280 <when value="number_input">
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281 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split."/>
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282 </when>
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283 </conditional>
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284 </xml>
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285
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286 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree.">
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287 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
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288 </xml>
0
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289
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290 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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291 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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292 </xml>
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293
7
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294 <xml name="subsample" token_help=" ">
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295 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@"/>
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296 </xml>
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297
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298 <xml name="presort">
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299 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
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300 <option value="auto" selected="true">auto</option>
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301 <option value="true">true</option>
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302 <option value="false">false</option>
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303 </param>
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304 </xml>
0
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305
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306 <!--Parameters-->
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307 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
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308 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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309 </xml>
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310
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311 <xml name="n_clusters" token_default_value="8">
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312 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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313 </xml>
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314
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315 <xml name="fit_intercept" token_checked="true">
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316 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
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317 </xml>
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318
7
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319 <xml name="n_jobs" token_default_value="1" token_label="The number of jobs to run in parallel for both fit and predict">
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320 <param argument="n_jobs" type="integer" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="If -1, then the number of jobs is set to the number of cores"/>
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321 </xml>
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322
0
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323 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
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324 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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325 </xml>
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326
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327 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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328 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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329 </xml>
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330
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331 <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results.">
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332 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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333 </xml>
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334
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335 <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution.">
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336 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
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337 </xml>
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338
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339 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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340 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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341 </xml>
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342
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343 <!--xml name="class_weight" token_default_value="" token_help_text="">
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344 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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345 </xml-->
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346
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347 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
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348 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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349 </xml>
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350
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351 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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352 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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353 </xml>
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354
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355 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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356 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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357 </xml>
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358
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359 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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360 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
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361 </xml>
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362
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363 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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364 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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365 </xml>
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366
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367 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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368 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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369 </xml>
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370
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371 <xml name="n_init" token_default_value="10" >
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372 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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373 </xml>
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374
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375 <xml name="init">
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376 <param argument="init" type="select" label="Centroid initialization method" help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids.">
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377 <option value="k-means++">k-means++</option>
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378 <option value="random">random</option>
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379 </param>
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380 </xml>
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381
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382 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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383 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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384 </xml>
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385
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386 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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387 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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388 </xml>
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389
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390 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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391 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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392 </xml>
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393
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394 <xml name="pos_label" token_default_value="">
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395 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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396 </xml>
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397
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398 <xml name="average">
1
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399 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
2
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400 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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401 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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402 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option>
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403 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option>
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404 <option value="None">None</option>
1
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405 <yield/>
0
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406 </param>
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407 </xml>
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408
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409 <xml name="beta">
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410 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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411 </xml>
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412
2
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413
0
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414 <!--Data interface-->
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415 <xml name="tabular_input">
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416 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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417 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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418 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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419 </xml>
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420
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421 <xml name="sample_cols" token_label1="File containing true class labels:" token_label2="File containing predicted class labels:" token_multiple1="False" token_multiple2="False" token_format1="tabular" token_format2="tabular" token_help1="" token_help2="">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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422 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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423 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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424 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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425 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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426 <yield/>
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427 </xml>
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428
12
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429 <xml name="samples_tabular" token_multiple1="false" token_multiple2="false">
2
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430 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
12
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431 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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432 <conditional name="column_selector_options_1">
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433 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
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434 </conditional>
2
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435 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/>
12
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436 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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437 <conditional name="column_selector_options_2">
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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438 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/>
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439 </conditional>
2
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440 <yield/>
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441 </xml>
1
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442
12
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443 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1">
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444 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:">
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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445 <option value="by_index_number" selected="true">Select columns by column index number(s)</option>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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446 <!--
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447 <option value="by_header_name">Select columns by column header name(s)</option>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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448 <option value="all_but_by_index_number">All columns but by column index number(s)</option>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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449 <option value="all_but_by_header_name">All columns but by column header name(s)</option>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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450 -->
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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451 <option value="all_columns">All columns</option>
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452 </param>
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453 <when value="by_index_number">
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454 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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455 </when>
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456 <when value="all_columns">
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457 </when>
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458 </xml>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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459
1
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parents: 0
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460 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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461 <conditional name="true_columns">
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462 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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463 <option value="tabular" selected="true">Tabular</option>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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464 <option value="sparse">Sparse</option>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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465 </param>
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466 <when value="tabular">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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467 <param name="infile1" type="data" label="@LABEL1@"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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468 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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469 </when>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents: 0
diff changeset
470 <when value="sparse">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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471 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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472 </when>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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473 </conditional>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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474 <conditional name="predicted_columns">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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475 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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476 <option value="tabular" selected="true">Tabular</option>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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477 <option value="sparse">Sparse</option>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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478 </param>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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479 <when value="tabular">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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480 <param name="infile2" type="data" label="@LABEL2@"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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481 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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482 </when>
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483 <when value="sparse">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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484 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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485 </when>
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486 </conditional>
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487 </xml>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents: 0
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488
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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489 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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490 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
9
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491 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
12
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492 <conditional name="column_selector_options_1">
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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493 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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494 </conditional>
1
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495 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
9
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496 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
12
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497 <conditional name="column_selector_options_2">
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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498 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/>
a31759a19a09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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499 </conditional>
1
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parents: 0
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500 </xml>
10d11b35b2fd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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501
0
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502 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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503 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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504 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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505 </repeat>
2
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506 </xml>
0
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507
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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508 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2="">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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509 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
510 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
511 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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512 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
513
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
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514 <xml name="sl_mixed_input">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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515 <conditional name="input_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
516 <param name="selected_input" type="select" label="Select input type:">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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517 <option value="tabular" selected="true">tabular data</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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518 <option value="sparse">sparse matrix</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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519 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
520 <when value="tabular">
2
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parents: 1
diff changeset
521 <expand macro="samples_tabular" multiple1="true"/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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522 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
523 <when value="sparse">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
524 <expand macro="sparse_target"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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525 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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526 </conditional>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
527 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
528
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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529 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
530 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
531 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
532
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
533
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
534 <!--Advanced options-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
535 <xml name="nn_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
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536 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
537 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
538 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
2
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diff changeset
539 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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540 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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541 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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542 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
543 <option value="auto" selected="true">Auto</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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544 <option value="ball_tree">BallTree</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
545 <option value="kd_tree">KDTree</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
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diff changeset
546 <option value="brute">Brute-force</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
547 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
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diff changeset
548 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
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549 <!--param name="metric"-->
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diff changeset
550 <!--param name="p"-->
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diff changeset
551 <!--param name="metric_params"-->
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552 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
553 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
554
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
555 <xml name="svc_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
556 <section name="options" title="Advanced Options" expanded="False">
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diff changeset
557 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
558 <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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559 <option value="rbf" selected="true">rbf</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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560 <option value="linear">linear</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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561 <option value="poly">poly</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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562 <option value="sigmoid">sigmoid</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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563 <option value="precomputed">precomputed</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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564 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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565 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
566 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
2
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567 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
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568 help="Independent term in kernel function. dafault: 0.0 "/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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569 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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570 label="Use the shrinking heuristic" help=" "/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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571 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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572 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
0
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573 <!-- param argument="cache_size"-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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574 <!--expand macro="class_weight"/-->
2
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575 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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576 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
577 <!--param argument="decision_function_shape"-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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578 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
579 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
580 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
581
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
582 <xml name="spectral_clustering_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
583 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
584 <expand macro="n_clusters"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
585 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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586 <option value="arpack" selected="true">arpack</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
587 <option value="lobpcg">lobpcg</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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588 <option value="amg">amg</option>
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diff changeset
589 <!--None-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
590 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
591 <expand macro="random_state"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
592 <expand macro="n_init"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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593 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
594 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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595 <option value="rbf" selected="true">RBF</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
596 <option value="precomputed">precomputed</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
597 <option value="nearest_neighbors">Nearset neighbors</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
598 </param>
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diff changeset
599 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
600 <!--param argument="eigen_tol"-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
601 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
602 <option value="kmeans" selected="true">kmeans</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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603 <option value="discretize">discretize</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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604 </param>
2
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605 <param argument="degree" type="integer" optional="true" value="3"
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606 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
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607 <param argument="coef0" type="integer" optional="true" value="1"
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608 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
0
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diff changeset
609 <!--param argument="kernel_params"-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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610 </section>
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611 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
612
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diff changeset
613 <xml name="minibatch_kmeans_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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614 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
615 <expand macro="n_clusters"/>
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616 <expand macro="init"/>
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diff changeset
617 <expand macro="n_init" default_value="3"/>
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618 <expand macro="max_iter" default_value="100"/>
2
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619 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
0
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diff changeset
620 <expand macro="random_state"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
621 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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622 <!--param argument="compute_labels"-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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623 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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624 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
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625 To disable, set max_no_improvement to None. "/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
626 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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627 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
628 </section>
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629 </xml>
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diff changeset
630
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diff changeset
631 <xml name="kmeans_advanced_options">
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632 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
633 <expand macro="n_clusters"/>
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diff changeset
634 <expand macro="init"/>
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diff changeset
635 <expand macro="n_init"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
636 <expand macro="max_iter"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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637 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
638 <!--param argument="precompute_distances"/-->
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diff changeset
639 <expand macro="random_state"/>
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
640 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
641 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
642 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
643
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
644 <xml name="birch_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
645 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
646 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
647 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
648 <expand macro="n_clusters" default_value="3"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
649 <!--param argument="compute_labels"/-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
650 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
651 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
652
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
653 <xml name="dbscan_advanced_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
654 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
655 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
656 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
657 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
658 <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors.">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
659 <option value="auto" selected="true">auto</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
660 <option value="ball_tree">ball_tree</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
661 <option value="kd_tree">kd_tree</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
662 <option value="brute">brute</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
663 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
664 <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
665 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
666 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
667
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
668 <xml name="clustering_algorithms_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
669 <conditional name="algorithm_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
670 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
671 <option value="KMeans" selected="true">KMeans</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
672 <option value="SpectralClustering">Spectral Clustering</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
673 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
674 <option value="DBSCAN">DBSCAN</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
675 <option value="Birch">Birch</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
676 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
677 <when value="KMeans">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
678 <expand macro="kmeans_advanced_options"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
679 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
680 <when value="DBSCAN">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
681 <expand macro="dbscan_advanced_options"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
682 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
683 <when value="Birch">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
684 <expand macro="birch_advanced_options"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
685 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
686 <when value="SpectralClustering">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
687 <expand macro="spectral_clustering_advanced_options"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
688 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
689 <when value="MiniBatchKMeans">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
690 <expand macro="minibatch_kmeans_advanced_options"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
691 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
692 </conditional>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
693 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
694
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
695 <xml name="distance_metrics">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
696 <param argument="metric" type="select" label="Distance metric" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
697 <option value="euclidean" selected="true">euclidean</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
698 <option value="cityblock">cityblock</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
699 <option value="cosine">cosine</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
700 <option value="l1">l1</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
701 <option value="l2">l2</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
702 <option value="manhattan">manhattan</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
703 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
704 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
705 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
706
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
707 <xml name="distance_nonsparse_metrics">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
708 <option value="braycurtis">braycurtis</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
709 <option value="canberra">canberra</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
710 <option value="chebyshev">chebyshev</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
711 <option value="correlation">correlation</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
712 <option value="dice">dice</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
713 <option value="hamming">hamming</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
714 <option value="jaccard">jaccard</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
715 <option value="kulsinski">kulsinski</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
716 <option value="mahalanobis">mahalanobis</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
717 <option value="matching">matching</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
718 <option value="minkowski">minkowski</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
719 <option value="rogerstanimoto">rogerstanimoto</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
720 <option value="russellrao">russellrao</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
721 <option value="seuclidean">seuclidean</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
722 <option value="sokalmichener">sokalmichener</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
723 <option value="sokalsneath">sokalsneath</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
724 <option value="sqeuclidean">sqeuclidean</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
725 <option value="yule">yule</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
726 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
727
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
728 <xml name="pairwise_kernel_metrics">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
729 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
730 <option value="rbf" selected="true">rbf</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
731 <option value="sigmoid">sigmoid</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
732 <option value="polynomial">polynomial</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
733 <option value="linear" selected="true">linear</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
734 <option value="chi2">chi2</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
735 <option value="additive_chi2">additive_chi2</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
736 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
737 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
738
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
739 <xml name="sparse_pairwise_metric_functions">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
740 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
741 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
742 <option value="pairwise_distances">Distance matrix</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
743 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
744 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
745 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
746 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
747
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
748 <xml name="pairwise_metric_functions">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
749 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
750 <option value="chi2_kernel">Exponential chi-squared kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
751 <option value="linear_kernel">Linear kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
752 <option value="manhattan_distances">L1 distances</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
753 <option value="pairwise_kernels">Kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
754 <option value="polynomial_kernel">Polynomial kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
755 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
756 <option value="laplacian_kernel">Laplacian kernel</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
757 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
758
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
759 <xml name="sparse_pairwise_condition">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
760 <when value="pairwise_distances">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
761 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
762 <expand macro="distance_metrics">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
763 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
764 </expand>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
765 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
766 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
767 <when value="euclidean_distances">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
768 <section name="options" title="Advanced Options" expanded="False">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
769 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
770 label="Return squared Euclidean distances" help=" "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
771 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
772 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
773 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
774
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
775 <xml name="argmin_distance_condition">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
776 <when value="pairwise_distances_argmin">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
777 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
778 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
779 <expand macro="distance_metrics">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
780 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
781 </expand>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
782 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
783 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
784 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
785 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
786
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
787 <xml name="sparse_preprocessors">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
788 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
789 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
790 <option value="Binarizer">Binarizer (Binarizes data)</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
791 <option value="Imputer">Imputer (Completes missing values)</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
792 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
793 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
794 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
795 </param>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
796 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
797
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
798 <xml name="sparse_preprocessor_options">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
799 <when value="Binarizer">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
800 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
801 <section name="options" title="Advanced Options" expanded="False">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
802 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
803 label="Use a copy of data for precomputing binarization" help=" "/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
804 <param argument="threshold" type="float" optional="true" value="0.0"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
805 label="Threshold"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
806 help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
807 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
808 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
809 <when value="Imputer">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
810 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
811 <section name="options" title="Advanced Options" expanded="False">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
812 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
813 label="Use a copy of data for precomputing imputation" help=" "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
814 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
815 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
816 <option value="median">Replace missing values using the median along the axis</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
817 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
818 </param>
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
819 <param argument="missing_values" type="text" optional="true" value="NaN"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
820 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
821 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
822 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
823 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
824 <option value="0" selected="true">Impute along columns</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
825 <option value="1">Impute along rows</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
826 </param-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
827 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
828 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
829 <when value="StandardScaler">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
830 <expand macro="multitype_input"/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
831 <section name="options" title="Advanced Options" expanded="False">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
832 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
833 label="Use a copy of data for performing inplace scaling" help=" "/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
834 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
835 label="Center the data before scaling" help=" "/>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
836 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
837 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
838 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
839 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
840 <when value="MaxAbsScaler">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
841 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
842 <section name="options" title="Advanced Options" expanded="False">
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
843 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
844 label="Use a copy of data for precomputing scaling" help=" "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
845 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
846 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
847 <when value="Normalizer">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
848 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
849 <section name="options" title="Advanced Options" expanded="False">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
850 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
851 <option value="l1" selected="true">l1</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
852 <option value="l2">l2</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
853 <option value="max">max</option>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
854 </param>
2
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
855 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
856 label="Use a copy of data for precomputing row normalization" help=" "/>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
857 </section>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
858 </when>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
859 <yield/>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
860 </xml>
11
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
861 <xml name="estimator_input_no_fit">
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
862 <expand macro="feature_selection_estimator" />
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
863 <conditional name="extra_estimator">
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
864 <expand macro="feature_selection_extra_estimator" />
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
865 <expand macro="feature_selection_estimator_choices" />
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
866 </conditional>
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
867 </xml>
10
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
868 <xml name="feature_selection_all">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
869 <conditional name="feature_selection_algorithms">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
870 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
871 <option value="SelectFromModel" selected="true">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
872 <option value="GenericUnivariateSelect" selected="true">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
873 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
874 <option value="SelectKBest">SelectKBest - Select features according to the k highest scores</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
875 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
876 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
877 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
878 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
879 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
880 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
881 <!--option value="chi2">Compute chi-squared stats between each non-negative feature and class</option-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
882 <!--option value="f_classif">Compute the ANOVA F-value for the provided sample</option-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
883 <!--option value="f_regression">Univariate linear regression tests</option-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
884 <!--option value="mutual_info_classif">Estimate mutual information for a discrete target variable</option-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
885 <!--option value="mutual_info_regression">Estimate mutual information for a continuous target variable</option-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
886 </param>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
887 <when value="SelectFromModel">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
888 <expand macro="feature_selection_estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
889 <conditional name="extra_estimator">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
890 <expand macro="feature_selection_extra_estimator" >
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
891 <option value="no_load">No, I will load a prefitted estimator</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
892 </expand>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
893 <expand macro="feature_selection_estimator_choices" >
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
894 <when value="no_load">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
895 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
896 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
897 </expand>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
898 </conditional>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
899 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
900 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
901 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
902 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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diff changeset
903 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
904 <when value="GenericUnivariateSelect">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
905 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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diff changeset
906 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
907 <param argument="mode" type="select" label="Feature selection mode">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
908 <option value="percentile">percentile</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
909 <option value="k_best">k_best</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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diff changeset
910 <option value="fpr">fpr</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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diff changeset
911 <option value="fdr">fdr</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
912 <option value="fwe">fwe</option>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
913 </param>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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diff changeset
914 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
915 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
916 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
917 <when value="SelectPercentile">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
918 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
919 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
920 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
921 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
922 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
923 <when value="SelectKBest">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
924 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
925 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
926 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
927 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
928 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
929 <when value="SelectFpr">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
930 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
931 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
932 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
933 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
934 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
935 <when value="SelectFdr">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
936 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
937 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
938 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
939 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
940 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
941 <when value="SelectFwe">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
942 <expand macro="feature_selection_score_function" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
943 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
944 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
945 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
946 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
947 <when value="RFE">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
948 <expand macro="feature_selection_estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
949 <conditional name="extra_estimator">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
950 <expand macro="feature_selection_extra_estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
951 <expand macro="feature_selection_estimator_choices" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
952 </conditional>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
953 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
954 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
955 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
956 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
957 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
958 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
959 <when value="RFECV">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
960 <expand macro="feature_selection_estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
961 <conditional name="extra_estimator">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
962 <expand macro="feature_selection_extra_estimator" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
963 <expand macro="feature_selection_estimator_choices" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
964 </conditional>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
965 <section name="options" title="Other Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
966 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
967 <param argument="cv" type="integer" value="" optional="true" label="cv" help="Determines the cross-validation splitting strategy" />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
968 <param argument="scoring" type="text" value="" optional="true" label="scoring" help="A string (see model evaluation documentation) or a scorer callable object / function with signature scorer(estimator, X, y)."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
969 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
970 <param argument="n_jobs" type="integer" value="1" label="n_jobs" help="Number of cores to run in parallel while fitting across folds. Defaults to 1 core."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
971 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
972 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
973 <when value="VarianceThreshold">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
974 <section name="options" title="Options" expanded="True">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
975 <param argument="threshold" type="float" value="" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
976 </section>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
977 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
978 <!--when value="chi2">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
979 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
980 <when value="f_classif">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
981 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
982 <when value="f_regression">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
983 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
984 <when value="mutual_info_classif">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
985 </when>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
986 <when value="mutual_info_regression">
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
987 </when-->
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
988 </conditional>
d466eb355094 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 9
diff changeset
989 </xml>
8
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
990 <xml name="feature_selection_score_function">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
991 <param argument="score_func" type="select" label="Select a score function">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
992 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
993 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
994 <option value="f_regression">f_regression - Univariate linear regression tests</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
995 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
996 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
997 </param>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
998 </xml>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
999 <xml name="feature_selection_estimator">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1000 <param argument="estimator" type="select" label="Select an estimator" help="The base estimator from which the transformer is built.">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1001 <option value="svm.SVR(kernel=&quot;linear&quot;)">svm.SVR(kernel=&quot;linear&quot;)</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1002 <option value="svm.SVC(kernel=&quot;linear&quot;)">svm.SVC(kernel=&quot;linear&quot;)</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1003 <option value="svm.LinearSVC(penalty=&quot;l1&quot;, dual=False, tol=1e-3)">svm.LinearSVC(penalty=&quot;l1&quot;, dual=False, tol=1e-3)</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1004 <option value="linear_model.LassoCV()">linear_model.LassoCV()</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1005 <option value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)">ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1006 </param>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1007 </xml>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1008 <xml name="feature_selection_extra_estimator">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1009 <param name="has_estimator" type="select" label="Does your estimator on the list above?">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1010 <option value="yes">Yes, my estimator is on the list</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1011 <option value="no">No, I need make a new estimator</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1012 <yield/>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1013 </param>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1014 </xml>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1015 <xml name="feature_selection_estimator_choices">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1016 <when value="yes">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1017 </when>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1018 <when value="no">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1019 <param name="new_estimator" type="text" value="" label="Make a new estimator" />
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1020 </when>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1021 <yield/>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1022 </xml>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1023 <xml name="feature_selection_methods">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1024 <conditional name="select_methods">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1025 <param name="selected_method" type="select" label="Select an operation">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1026 <option value="fit_transform">fit_transform - Fit to data, then transform it</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1027 <option value="get_support">get_support - Get a mask, or integer index, of the features selected</option>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1028 </param>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1029 <when value="fit_transform">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1030 <!--**fit_params-->
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1031 </when>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1032 <when value="get_support">
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 7
diff changeset
1033 <param name="indices" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Indices" help="If True, the return value will be an array of integers, rather than a boolean mask."/>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1034 </when>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1035 </conditional>
699713c045f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 7
diff changeset
1036 </xml>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
1037
9
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1038 <xml name="model_validation_common_options">
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1039 <param argument="cv" type="integer" value="" optional="true" label="cv" help="The number of folds in a (Stratified)KFold" />
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1040 <expand macro="n_jobs"/>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1041 <expand macro="verbose"/>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1042 <yield/>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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parents: 8
diff changeset
1043 </xml>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1044
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1045 <xml name="scoring">
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1046 <param argument="scoring" type="text" value="" optional="true" label="scoring" help="A metric used to evaluate the estimator"/>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1047 </xml>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1048
11
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
1049 <xml name="pre_dispatch" token_type="text" token_default_value="all" token_help="Number of predispatched jobs for parallel execution">
d8fa28fb18f8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 10
diff changeset
1050 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/>
9
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1051 </xml>
983d9f614b17 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 8
diff changeset
1052
2
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bgruening
parents: 1
diff changeset
1053 <!-- Outputs -->
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 1
diff changeset
1054
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1055 <xml name="output">
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 1
diff changeset
1056 <outputs>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1057 <data format="tabular" name="outfile_predict">
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1058 <filter>selected_tasks['selected_task'] == 'load'</filter>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1059 </data>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1060 <data format="zip" name="outfile_fit">
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1061 <filter>selected_tasks['selected_task'] == 'train'</filter>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1062 </data>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1063 </outputs>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1064 </xml>
43075be4044b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 1
diff changeset
1065
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1066
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
1067 <!--Citations-->
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1068 <xml name="eden_citation">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
1069 <citations>
5
1a224ebdf9a8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 99231ce3ef238975a6614926f2fa6326b9454ee8
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parents: 4
diff changeset
1070 <citation type="doi">10.5281/zenodo.15094</citation>
0
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents:
diff changeset
1071 </citations>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1072 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1073
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1074 <xml name="sklearn_citation">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1075 <citations>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1076 <citation type="bibtex">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1077 @article{scikit-learn,
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1078 title={Scikit-learn: Machine Learning in {P}ython},
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1079 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1080 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1081 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1082 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1083 journal={Journal of Machine Learning Research},
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1084 volume={12},
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1085 pages={2825--2830},
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1086 year={2011}
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1087 url = {https://github.com/scikit-learn/scikit-learn}
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1088 }
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1089 </citation>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1090 </citations>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1091 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1092
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1093 <xml name="scipy_citation">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1094 <citations>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1095 <citation type="bibtex">
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
diff changeset
1096 @Misc{,
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents:
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1097 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
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1098 title = {{SciPy}: Open source scientific tools for {Python}},
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1099 year = {2001--},
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1100 url = "http://www.scipy.org/",
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1101 note = {[Online; accessed 2016-04-09]}
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1102 }
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1103 </citation>
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1104 </citations>
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1105 </xml>
12b2bef577d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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1106
2
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1107 </macros>