Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate main_macros.xml @ 15:d093a5421bba draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
author bgruening
date Wed, 30 May 2018 08:20:52 -0400
parents 9e4bda259863
children cd661d6d20c4
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dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
1 <macros>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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2 <token name="@VERSION@">0.9</token>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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3
5
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents: 3
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4 <token name="@COLUMNS_FUNCTION@">
14
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
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5 def read_columns(f, c, return_df=False, **args):
8
c90db9c3f7d0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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6 data = pandas.read_csv(f, **args)
5
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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7 cols = c.split (',')
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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8 cols = map(int, cols)
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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9 cols = list(map(lambda x: x - 1, cols))
14
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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10 data = data.iloc[:,cols]
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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11 y = data.values
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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12 if return_df:
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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13 return y, data
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
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14 else:
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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15 return y
5
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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16 return y
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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17 </token>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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18
15
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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19 ## generate an instance for one of sklearn.feature_selection classes
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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20 ## must call "@COLUMNS_FUNCTION@"
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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21 <token name="@FEATURE_SELECTOR_FUNCTION@">
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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22 def feature_selector(inputs):
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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23 selector = inputs["selected_algorithm"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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24 selector = getattr(sklearn.feature_selection, selector)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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25 options = inputs["options"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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26
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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27 if inputs['selected_algorithm'] == 'SelectFromModel':
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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28 if not options['threshold'] or options['threshold'] == 'None':
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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29 options['threshold'] = None
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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30 if 'extra_estimator' in inputs and inputs['extra_estimator']['has_estimator'] == 'no_load':
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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31 fitted_estimator = pickle.load(open("inputs['extra_estimator']['fitted_estimator']", 'r'))
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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32 new_selector = selector(fitted_estimator, prefit=True, **options)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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33 else:
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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34 estimator=inputs["estimator"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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35 if inputs["extra_estimator"]["has_estimator"]=='no':
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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36 estimator=inputs["extra_estimator"]["new_estimator"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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37 estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
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38 new_selector = selector(estimator, **options)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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39
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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40 elif inputs['selected_algorithm'] in ['RFE', 'RFECV']:
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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41 if 'scoring' in options and (not options['scoring'] or options['scoring'] == 'None'):
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
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42 options['scoring'] = None
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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43 estimator=inputs["estimator"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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44 if inputs["extra_estimator"]["has_estimator"]=='no':
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
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45 estimator=inputs["extra_estimator"]["new_estimator"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
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46 estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
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47 new_selector = selector(estimator, **options)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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48
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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49 elif inputs['selected_algorithm'] == "VarianceThreshold":
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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50 new_selector = selector(**options)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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51
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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52 else:
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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53 score_func = inputs["score_func"]
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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54 score_func = getattr(sklearn.feature_selection, score_func)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
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55 new_selector = selector(score_func, **options)
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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56
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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57 return new_selector
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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58 </token>
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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59
0
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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60 <xml name="python_requirements">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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61 <requirements>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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62 <requirement type="package" version="2.7">python</requirement>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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63 <requirement type="package" version="0.19.1">scikit-learn</requirement>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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64 <requirement type="package" version="0.22.0">pandas</requirement>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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65 <yield />
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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66 </requirements>
0
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67 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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68
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69 <xml name="macro_stdio">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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70 <stdio>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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71 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
0
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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72 </stdio>
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73 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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74
2
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75
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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76 <!--Generic interface-->
0
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77 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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78 <conditional name="selected_tasks">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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79 <param name="selected_task" type="select" label="Select a Classification Task">
2
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80 <option value="train" selected="true">Train a model</option>
0
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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81 <option value="load">Load a model and predict</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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82 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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83 <when value="load">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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84 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
0
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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85 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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86 <conditional name="prediction_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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87 <param name="prediction_option" type="select" label="Select the type of prediction">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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88 <option value="predict">Predict class labels</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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89 <option value="advanced">Include advanced options</option>
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90 </param>
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91 <when value="predict">
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92 </when>
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93 <when value="advanced">
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94 </when>
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95 </conditional>
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96 </when>
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97 <when value="train">
3
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98 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
0
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99 <conditional name="selected_algorithms">
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100 <yield />
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101 </conditional>
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102 </when>
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103 </conditional>
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104 </xml>
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105
2
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106 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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107 <conditional name="selected_tasks">
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108 <param name="selected_task" type="select" label="Select a Classification Task">
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109 <option value="train" selected="true">Train a model</option>
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110 <option value="load">Load a model and predict</option>
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111 </param>
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112 <when value="load">
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113 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
2
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114 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
11
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115 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
2
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116 <conditional name="prediction_options">
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117 <param name="prediction_option" type="select" label="Select the type of prediction">
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118 <option value="predict">Predict class labels</option>
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119 <option value="advanced">Include advanced options</option>
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120 </param>
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121 <when value="predict">
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122 </when>
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123 <when value="advanced">
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124 </when>
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125 </conditional>
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126 </when>
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127 <when value="train">
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128 <conditional name="selected_algorithms">
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129 <yield />
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130 </conditional>
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131 </when>
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132 </conditional>
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133 </xml>
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134
0
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135 <xml name="advanced_section">
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136 <section name="options" title="Advanced Options" expanded="False">
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137 <yield />
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138 </section>
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139 </xml>
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140
2
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141
6
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142 <!--Generalized Linear Models-->
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143 <xml name="loss" token_help=" " token_select="false">
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144 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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145 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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146 <option value="huber">huber</option>
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147 <option value="epsilon_insensitive">epsilon insensitive</option>
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148 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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149 <yield/>
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150 </param>
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151 </xml>
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152
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153 <xml name="penalty" token_help=" ">
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154 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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155 <option value="l2" selected="true">l2</option>
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156 <option value="l1">l1</option>
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157 <option value="elasticnet">elastic net</option>
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158 <option value="none">none</option>
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159 <yield/>
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160 </param>
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161 </xml>
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162
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163 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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164 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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165 </xml>
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166
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167 <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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168 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
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169 </xml>
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170
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171 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
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172 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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173 <option value="optimal" selected="@SELECTED1@">optimal</option>
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174 <option value="constant">constant</option>
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175 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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176 <yield/>
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177 </param>
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178 </xml>
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179
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180 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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181 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
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182 </xml>
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183
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184 <xml name="power_t" token_default_value="0.5" token_help=" ">
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185 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
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186 </xml>
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187
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188 <xml name="normalize" token_checked="false" token_help=" ">
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189 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
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190 </xml>
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191
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192 <xml name="copy_X" token_checked="true" token_help=" ">
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193 <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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194 </xml>
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195
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196 <xml name="ridge_params">
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197 <expand macro="normalize"/>
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198 <expand macro="alpha" default_value="1.0"/>
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199 <expand macro="fit_intercept"/>
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200 <expand macro="max_iter" default_value=""/>
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201 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
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202 <!--class_weight-->
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203 <expand macro="copy_X"/>
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204 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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205 <option value="auto" selected="true">auto</option>
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206 <option value="svd">svd</option>
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207 <option value="cholesky">cholesky</option>
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208 <option value="lsqr">lsqr</option>
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209 <option value="sparse_cg">sparse_cg</option>
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210 <option value="sag">sag</option>
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211 </param>
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212 <expand macro="random_state"/>
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213 </xml>
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214
2
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215 <!--Ensemble methods-->
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216 <xml name="n_estimators" token_default_value="10" token_help=" ">
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217 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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218 </xml>
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219
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220 <xml name="max_depth" token_default_value="" token_help=" ">
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221 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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222 </xml>
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223
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224 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
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225 <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@"/>
2
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226 </xml>
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227
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228 <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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229 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
2
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230 </xml>
6
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231
2
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232 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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233 <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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234 </xml>
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235
2
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236 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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237 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
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238 </xml>
2
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239
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240 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
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241 <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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242 </xml>
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243
2
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244 <xml name="bootstrap" token_checked="true" token_help=" ">
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245 <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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246 </xml>
2
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247
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248 <xml name="criterion" token_help=" ">
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249 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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250 <option value="gini" selected="true">Gini impurity</option>
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251 <option value="entropy">Information gain</option>
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252 <yield/>
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253 </param>
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254 </xml>
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255
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256 <xml name="criterion2" token_help="">
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257 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
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258 <option value="mse">mse - mean squared error</option>
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259 <option value="mae">mae - mean absolute error</option>
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260 <yield/>
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261 </param>
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262 </xml>
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263
6
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264 <xml name="oob_score" token_checked="false" token_help=" ">
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265 <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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266 </xml>
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267
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268 <xml name="max_features">
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269 <conditional name="select_max_features">
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270 <param argument="max_features" type="select" label="max_features">
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271 <option value="auto" selected="true">auto - max_features=n_features</option>
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272 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
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273 <option value="log2">log2 - max_features=log2(n_features)</option>
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274 <option value="number_input">I want to type the number in or input None type</option>
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275 </param>
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276 <when value="auto">
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277 </when>
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278 <when value="sqrt">
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279 </when>
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280 <when value="log2">
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281 </when>
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282 <when value="number_input">
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283 <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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284 </when>
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285 </conditional>
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286 </xml>
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287
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288 <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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289 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
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290 </xml>
2
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291
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292 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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293 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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294 </xml>
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295
11
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296 <xml name="subsample" token_help=" ">
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297 <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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298 </xml>
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299
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300 <xml name="presort">
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301 <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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302 <option value="auto" selected="true">auto</option>
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303 <option value="true">true</option>
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304 <option value="false">false</option>
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305 </param>
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306 </xml>
2
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307
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308 <!--Parameters-->
0
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309 <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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310 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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311 </xml>
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312
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313 <xml name="n_clusters" token_default_value="8">
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314 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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315 </xml>
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316
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317 <xml name="fit_intercept" token_checked="true">
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318 <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."/>
0
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319 </xml>
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320
11
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321 <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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322 <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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323 </xml>
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324
0
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325 <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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326 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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327 </xml>
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328
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329 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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330 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
0
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331 </xml>
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332
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333 <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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334 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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335 </xml>
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336
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337 <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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338 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
0
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339 </xml>
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340
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341 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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342 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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343 </xml>
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344
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345 <!--xml name="class_weight" token_default_value="" token_help_text="">
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346 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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347 </xml-->
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348
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349 <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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350 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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351 </xml>
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352
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353 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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354 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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355 </xml>
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356
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357 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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358 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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359 </xml>
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360
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361 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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362 <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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363 </xml>
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364
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365 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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366 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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367 </xml>
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368
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369 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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370 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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371 </xml>
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372
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373 <xml name="n_init" token_default_value="10" >
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374 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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375 </xml>
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376
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377 <xml name="init">
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378 <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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379 <option value="k-means++">k-means++</option>
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380 <option value="random">random</option>
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381 </param>
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382 </xml>
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383
1
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384 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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385 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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386 </xml>
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387
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388 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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389 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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390 </xml>
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391
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392 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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393 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
2
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394 </xml>
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395
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396 <xml name="pos_label" token_default_value="">
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397 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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398 </xml>
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399
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400 <xml name="average">
5
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401 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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402 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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403 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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404 <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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405 <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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406 <option value="None">None</option>
5
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407 <yield/>
2
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408 </param>
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409 </xml>
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410
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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411 <xml name="beta">
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412 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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413 </xml>
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414
6
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415
2
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416 <!--Data interface-->
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417 <xml name="tabular_input">
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418 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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419 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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420 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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421 </xml>
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422
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423 <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="">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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424 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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425 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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426 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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427 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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428 <yield/>
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429 </xml>
1
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430
6
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431 <xml name="samples_tabular" token_multiple1="False" token_multiple2="False">
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432 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
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433 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
6
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434 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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435 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/>
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436 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
6
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437 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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438 <yield/>
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439 </xml>
5
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440
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441 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
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442 <conditional name="true_columns">
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443 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
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444 <option value="tabular" selected="true">Tabular</option>
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445 <option value="sparse">Sparse</option>
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446 </param>
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447 <when value="tabular">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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448 <param name="infile1" type="data" label="@LABEL1@"/>
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parents: 3
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449 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents: 3
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450 </when>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents: 3
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451 <when value="sparse">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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452 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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453 </when>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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454 </conditional>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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455 <conditional name="predicted_columns">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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456 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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457 <option value="tabular" selected="true">Tabular</option>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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458 <option value="sparse">Sparse</option>
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459 </param>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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460 <when value="tabular">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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461 <param name="infile2" type="data" label="@LABEL2@"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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462 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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463 </when>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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464 <when value="sparse">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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465 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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466 </when>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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467 </conditional>
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468 </xml>
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469
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470 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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471 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
13
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472 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
5
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473 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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474 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
13
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475 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
5
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476 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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477 </xml>
7dc70333811d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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478
1
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479 <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.">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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480 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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481 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
0
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482 </repeat>
6
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483 </xml>
0
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484
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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485 <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="">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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486 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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487 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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488 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
0
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diff changeset
489 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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490
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
491 <xml name="sl_mixed_input">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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492 <conditional name="input_options">
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diff changeset
493 <param name="selected_input" type="select" label="Select input type:">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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494 <option value="tabular" selected="true">tabular data</option>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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495 <option value="sparse">sparse matrix</option>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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496 </param>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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497 <when value="tabular">
6
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diff changeset
498 <expand macro="samples_tabular" multiple1="true"/>
2
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diff changeset
499 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
500 <when value="sparse">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
501 <expand macro="sparse_target"/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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502 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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503 </conditional>
0
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504 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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505
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
506 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
507 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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508 </xml>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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509
0
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
510
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
511 <!--Advanced options-->
0
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512 <xml name="nn_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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513 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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514 <yield/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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515 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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diff changeset
516 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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517 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
0
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518 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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519 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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520 <option value="auto" selected="true">Auto</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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521 <option value="ball_tree">BallTree</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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522 <option value="kd_tree">KDTree</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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523 <option value="brute">Brute-force</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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524 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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525 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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526 <!--param name="metric"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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527 <!--param name="p"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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528 <!--param name="metric_params"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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529 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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530 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
531
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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532 <xml name="svc_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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533 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
534 <yield/>
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535 <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.">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
536 <option value="rbf" selected="true">rbf</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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537 <option value="linear">linear</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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538 <option value="poly">poly</option>
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539 <option value="sigmoid">sigmoid</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
540 <option value="precomputed">precomputed</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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541 </param>
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542 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
543 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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diff changeset
544 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
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545 help="Independent term in kernel function. dafault: 0.0 "/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
546 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
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547 label="Use the shrinking heuristic" help=" "/>
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548 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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549 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
0
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diff changeset
550 <!-- param argument="cache_size"-->
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diff changeset
551 <!--expand macro="class_weight"/-->
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diff changeset
552 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
0
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diff changeset
553 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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554 <!--param argument="decision_function_shape"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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555 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
556 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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557 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
558
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
559 <xml name="spectral_clustering_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
560 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
561 <expand macro="n_clusters"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
562 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
563 <option value="arpack" selected="true">arpack</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
564 <option value="lobpcg">lobpcg</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
565 <option value="amg">amg</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
566 <!--None-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
567 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
568 <expand macro="random_state"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
569 <expand macro="n_init"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
570 <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''."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
571 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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572 <option value="rbf" selected="true">RBF</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
573 <option value="precomputed">precomputed</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
574 <option value="nearest_neighbors">Nearset neighbors</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
575 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
576 <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''"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
577 <!--param argument="eigen_tol"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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578 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
579 <option value="kmeans" selected="true">kmeans</option>
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580 <option value="discretize">discretize</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
581 </param>
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diff changeset
582 <param argument="degree" type="integer" optional="true" value="3"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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583 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
584 <param argument="coef0" type="integer" optional="true" value="1"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
585 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
0
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diff changeset
586 <!--param argument="kernel_params"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
587 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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588 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
589
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
590 <xml name="minibatch_kmeans_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
591 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
592 <expand macro="n_clusters"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
593 <expand macro="init"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
594 <expand macro="n_init" default_value="3"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
595 <expand macro="max_iter" default_value="100"/>
6
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diff changeset
596 <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
597 <expand macro="random_state"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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598 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
599 <!--param argument="compute_labels"-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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600 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
601 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
602 To disable, set max_no_improvement to None. "/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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603 <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 )"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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604 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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605 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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606 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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607
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
608 <xml name="kmeans_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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609 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
610 <expand macro="n_clusters"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
611 <expand macro="init"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
612 <expand macro="n_init"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
613 <expand macro="max_iter"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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614 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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615 <!--param argument="precompute_distances"/-->
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616 <expand macro="random_state"/>
6
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617 <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
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618 </section>
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619 </xml>
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620
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
621 <xml name="birch_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
622 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
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623 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
624 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
625 <expand macro="n_clusters" default_value="3"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
626 <!--param argument="compute_labels"/-->
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
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627 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
628 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
629
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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parents:
diff changeset
630 <xml name="dbscan_advanced_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
631 <section name="options" title="Advanced Options" expanded="False">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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632 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
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633 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
634 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
635 <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.">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
636 <option value="auto" selected="true">auto</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
637 <option value="ball_tree">ball_tree</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
638 <option value="kd_tree">kd_tree</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
639 <option value="brute">brute</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
640 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
641 <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."/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
642 </section>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
643 </xml>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
644
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
645 <xml name="clustering_algorithms_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
646 <conditional name="algorithm_options">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
647 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
648 <option value="KMeans" selected="true">KMeans</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
649 <option value="SpectralClustering">Spectral Clustering</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
650 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
651 <option value="DBSCAN">DBSCAN</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
652 <option value="Birch">Birch</option>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
653 </param>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
654 <when value="KMeans">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
655 <expand macro="kmeans_advanced_options"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
656 </when>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
657 <when value="DBSCAN">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
658 <expand macro="dbscan_advanced_options"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
659 </when>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
660 <when value="Birch">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
661 <expand macro="birch_advanced_options"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
662 </when>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
663 <when value="SpectralClustering">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
664 <expand macro="spectral_clustering_advanced_options"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
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diff changeset
665 </when>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
666 <when value="MiniBatchKMeans">
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
667 <expand macro="minibatch_kmeans_advanced_options"/>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
668 </when>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
669 </conditional>
dac8a9712939 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
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670 </xml>
1
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
671
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
672 <xml name="distance_metrics">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
673 <param argument="metric" type="select" label="Distance metric" help=" ">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
674 <option value="euclidean" selected="true">euclidean</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
675 <option value="cityblock">cityblock</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
676 <option value="cosine">cosine</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
677 <option value="l1">l1</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
678 <option value="l2">l2</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
679 <option value="manhattan">manhattan</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
680 <yield/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
681 </param>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
682 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
683
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
684 <xml name="distance_nonsparse_metrics">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
685 <option value="braycurtis">braycurtis</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
686 <option value="canberra">canberra</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
687 <option value="chebyshev">chebyshev</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
688 <option value="correlation">correlation</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
689 <option value="dice">dice</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
690 <option value="hamming">hamming</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
691 <option value="jaccard">jaccard</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
692 <option value="kulsinski">kulsinski</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
693 <option value="mahalanobis">mahalanobis</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
694 <option value="matching">matching</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
695 <option value="minkowski">minkowski</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
696 <option value="rogerstanimoto">rogerstanimoto</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
697 <option value="russellrao">russellrao</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
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698 <option value="seuclidean">seuclidean</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
699 <option value="sokalmichener">sokalmichener</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
700 <option value="sokalsneath">sokalsneath</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
701 <option value="sqeuclidean">sqeuclidean</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
702 <option value="yule">yule</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
703 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
704
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
705 <xml name="pairwise_kernel_metrics">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
706 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
707 <option value="rbf" selected="true">rbf</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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diff changeset
708 <option value="sigmoid">sigmoid</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
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709 <option value="polynomial">polynomial</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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710 <option value="linear" selected="true">linear</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
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711 <option value="chi2">chi2</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
712 <option value="additive_chi2">additive_chi2</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
713 </param>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
714 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
715
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
716 <xml name="sparse_pairwise_metric_functions">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
717 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
718 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
719 <option value="pairwise_distances">Distance matrix</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
720 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
721 <yield/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
722 </param>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
723 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
724
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
725 <xml name="pairwise_metric_functions">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
726 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
727 <option value="chi2_kernel">Exponential chi-squared kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
728 <option value="linear_kernel">Linear kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
729 <option value="manhattan_distances">L1 distances</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
730 <option value="pairwise_kernels">Kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
731 <option value="polynomial_kernel">Polynomial kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
732 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
733 <option value="laplacian_kernel">Laplacian kernel</option>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
734 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
735
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
736 <xml name="sparse_pairwise_condition">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
737 <when value="pairwise_distances">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
738 <section name="options" title="Advanced Options" expanded="False">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
739 <expand macro="distance_metrics">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
740 <yield/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
741 </expand>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
742 </section>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
743 </when>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
744 <when value="euclidean_distances">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
745 <section name="options" title="Advanced Options" expanded="False">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
746 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
747 label="Return squared Euclidean distances" help=" "/>
1
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
748 </section>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
749 </when>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
750 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
751
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
752 <xml name="argmin_distance_condition">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
753 <when value="pairwise_distances_argmin">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
754 <section name="options" title="Advanced Options" expanded="False">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
755 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
756 <expand macro="distance_metrics">
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
757 <yield/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
758 </expand>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
759 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
760 </section>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
761 </when>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
762 </xml>
d938b80a954f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
763
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
764 <xml name="sparse_preprocessors">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
765 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
766 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
767 <option value="Binarizer">Binarizer (Binarizes data)</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
768 <option value="Imputer">Imputer (Completes missing values)</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
769 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
770 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
771 <yield/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
772 </param>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
773 </xml>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
774
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
775 <xml name="sparse_preprocessor_options">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
776 <when value="Binarizer">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
777 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
778 <section name="options" title="Advanced Options" expanded="False">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
779 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
780 label="Use a copy of data for precomputing binarization" help=" "/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
781 <param argument="threshold" type="float" optional="true" value="0.0"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
782 label="Threshold"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
783 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. "/>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
784 </section>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
785 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
786 <when value="Imputer">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
787 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
788 <section name="options" title="Advanced Options" expanded="False">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
789 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
790 label="Use a copy of data for precomputing imputation" help=" "/>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
791 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
792 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
793 <option value="median">Replace missing values using the median along the axis</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
794 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
795 </param>
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
796 <param argument="missing_values" type="text" optional="true" value="NaN"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
797 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
798 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
799 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
800 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
801 <option value="0" selected="true">Impute along columns</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
802 <option value="1">Impute along rows</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
803 </param-->
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parents: 2
diff changeset
804 </section>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
805 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
806 <when value="StandardScaler">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
807 <expand macro="multitype_input"/>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
808 <section name="options" title="Advanced Options" expanded="False">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
809 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
810 label="Use a copy of data for performing inplace scaling" help=" "/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
811 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
812 label="Center the data before scaling" help=" "/>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
813 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
814 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
815 </section>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
816 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
817 <when value="MaxAbsScaler">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
818 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
819 <section name="options" title="Advanced Options" expanded="False">
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
820 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
821 label="Use a copy of data for precomputing scaling" help=" "/>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
822 </section>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
823 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
824 <when value="Normalizer">
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
825 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
826 <section name="options" title="Advanced Options" expanded="False">
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
827 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
828 <option value="l1" selected="true">l1</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
829 <option value="l2">l2</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
830 <option value="max">max</option>
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
831 </param>
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
832 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
833 label="Use a copy of data for precomputing row normalization" help=" "/>
3
a8951d76b7d2 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
834 </section>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
835 </when>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
836 <yield/>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
837 </xml>
15
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
838 <xml name="estimator_input_no_fit">
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
839 <expand macro="feature_selection_estimator" />
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
840 <conditional name="extra_estimator">
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
841 <expand macro="feature_selection_extra_estimator" />
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
842 <expand macro="feature_selection_estimator_choices" />
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
843 </conditional>
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
844 </xml>
14
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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parents: 13
diff changeset
845 <xml name="feature_selection_all">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
846 <conditional name="feature_selection_algorithms">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
847 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
848 <option value="SelectFromModel" selected="true">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
849 <option value="GenericUnivariateSelect" selected="true">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
850 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
851 <option value="SelectKBest">SelectKBest - Select features according to the k highest scores</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
852 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
853 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
854 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
855 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
856 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
857 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
858 <!--option value="chi2">Compute chi-squared stats between each non-negative feature and class</option-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
859 <!--option value="f_classif">Compute the ANOVA F-value for the provided sample</option-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
860 <!--option value="f_regression">Univariate linear regression tests</option-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
861 <!--option value="mutual_info_classif">Estimate mutual information for a discrete target variable</option-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
862 <!--option value="mutual_info_regression">Estimate mutual information for a continuous target variable</option-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
863 </param>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
864 <when value="SelectFromModel">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
865 <expand macro="feature_selection_estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
866 <conditional name="extra_estimator">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
867 <expand macro="feature_selection_extra_estimator" >
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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parents: 13
diff changeset
868 <option value="no_load">No, I will load a prefitted estimator</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
869 </expand>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
870 <expand macro="feature_selection_estimator_choices" >
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
871 <when value="no_load">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
872 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
873 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
874 </expand>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
875 </conditional>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
876 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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parents: 13
diff changeset
877 <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'." />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
878 <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. " />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
879 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
880 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
881 <when value="GenericUnivariateSelect">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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parents: 13
diff changeset
882 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
883 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
884 <param argument="mode" type="select" label="Feature selection mode">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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parents: 13
diff changeset
885 <option value="percentile">percentile</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
886 <option value="k_best">k_best</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
887 <option value="fpr">fpr</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
888 <option value="fdr">fdr</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
889 <option value="fwe">fwe</option>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
890 </param>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
891 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
892 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
893 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
894 <when value="SelectPercentile">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
895 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
896 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
897 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
898 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
899 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
900 <when value="SelectKBest">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
901 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
902 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
903 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
904 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
905 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
906 <when value="SelectFpr">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
907 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
908 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
909 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
910 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
911 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
912 <when value="SelectFdr">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
913 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
914 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
915 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
916 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
917 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
918 <when value="SelectFwe">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
919 <expand macro="feature_selection_score_function" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
920 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
921 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
922 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
923 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
924 <when value="RFE">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
925 <expand macro="feature_selection_estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
926 <conditional name="extra_estimator">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
927 <expand macro="feature_selection_extra_estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
928 <expand macro="feature_selection_estimator_choices" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
929 </conditional>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
930 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
931 <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." />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
932 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
933 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
934 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
935 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
936 <when value="RFECV">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
937 <expand macro="feature_selection_estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
938 <conditional name="extra_estimator">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
939 <expand macro="feature_selection_extra_estimator" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
940 <expand macro="feature_selection_estimator_choices" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
941 </conditional>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
942 <section name="options" title="Other Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
943 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
944 <param argument="cv" type="integer" value="" optional="true" label="cv" help="Determines the cross-validation splitting strategy" />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
945 <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)."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
946 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
947 <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."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
948 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
949 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
950 <when value="VarianceThreshold">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
951 <section name="options" title="Options" expanded="True">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
952 <param argument="threshold" type="float" value="" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
953 </section>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
954 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
955 <!--when value="chi2">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
956 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
957 <when value="f_classif">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
958 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
959 <when value="f_regression">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
960 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
961 <when value="mutual_info_classif">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
962 </when>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
963 <when value="mutual_info_regression">
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
964 </when-->
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
965 </conditional>
9e4bda259863 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 13
diff changeset
966 </xml>
12
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
967 <xml name="feature_selection_score_function">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
968 <param argument="score_func" type="select" label="Select a score function">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
969 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
970 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
971 <option value="f_regression">f_regression - Univariate linear regression tests</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
972 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
973 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
974 </param>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
975 </xml>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
976 <xml name="feature_selection_estimator">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
977 <param argument="estimator" type="select" label="Select an estimator" help="The base estimator from which the transformer is built.">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
978 <option value="svm.SVR(kernel=&quot;linear&quot;)">svm.SVR(kernel=&quot;linear&quot;)</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
979 <option value="svm.SVC(kernel=&quot;linear&quot;)">svm.SVC(kernel=&quot;linear&quot;)</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
980 <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>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
981 <option value="linear_model.LassoCV()">linear_model.LassoCV()</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
982 <option value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)">ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
983 </param>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
984 </xml>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
985 <xml name="feature_selection_extra_estimator">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
986 <param name="has_estimator" type="select" label="Does your estimator on the list above?">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
987 <option value="yes">Yes, my estimator is on the list</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
988 <option value="no">No, I need make a new estimator</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
989 <yield/>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
990 </param>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
991 </xml>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
992 <xml name="feature_selection_estimator_choices">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
993 <when value="yes">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
994 </when>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
995 <when value="no">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
996 <param name="new_estimator" type="text" value="" label="Make a new estimator" />
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
997 </when>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
998 <yield/>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
999 </xml>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1000 <xml name="feature_selection_methods">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1001 <conditional name="select_methods">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1002 <param name="selected_method" type="select" label="Select an operation">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1003 <option value="fit_transform">fit_transform - Fit to data, then transform it</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1004 <option value="get_support">get_support - Get a mask, or integer index, of the features selected</option>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1005 </param>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1006 <when value="fit_transform">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1007 <!--**fit_params-->
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1008 </when>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
1009 <when value="get_support">
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents: 11
diff changeset
1010 <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."/>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
1011 </when>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
1012 </conditional>
916f4ac50342 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 11
diff changeset
1013 </xml>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1014
13
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1015 <xml name="model_validation_common_options">
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1016 <param argument="cv" type="integer" value="" optional="true" label="cv" help="The number of folds in a (Stratified)KFold" />
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1017 <expand macro="n_jobs"/>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1018 <expand macro="verbose"/>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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parents: 12
diff changeset
1019 <yield/>
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bgruening
parents: 12
diff changeset
1020 </xml>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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parents: 12
diff changeset
1021
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1022 <xml name="scoring">
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1023 <param argument="scoring" type="text" value="" optional="true" label="scoring" help="A metric used to evaluate the estimator"/>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1024 </xml>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1025
15
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
1026 <xml name="pre_dispatch" token_type="text" token_default_value="all" token_help="Number of predispatched jobs for parallel execution">
d093a5421bba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 14
diff changeset
1027 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/>
13
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1028 </xml>
9b2abcd632ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 12
diff changeset
1029
6
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1030 <!-- Outputs -->
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 5
diff changeset
1031
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1032 <xml name="output">
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1033 <outputs>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 5
diff changeset
1034 <data format="tabular" name="outfile_predict">
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1035 <filter>selected_tasks['selected_task'] == 'load'</filter>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1036 </data>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1037 <data format="zip" name="outfile_fit">
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1038 <filter>selected_tasks['selected_task'] == 'train'</filter>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1039 </data>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1040 </outputs>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1041 </xml>
4edccd1eaaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 5
diff changeset
1042
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1043
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1044 <!--Citations-->
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1045 <xml name="eden_citation">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1046 <citations>
9
d310d90465f8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 99231ce3ef238975a6614926f2fa6326b9454ee8
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parents: 8
diff changeset
1047 <citation type="doi">10.5281/zenodo.15094</citation>
2
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1048 </citations>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1049 </xml>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1050
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1051 <xml name="sklearn_citation">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1052 <citations>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1053 <citation type="bibtex">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1054 @article{scikit-learn,
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1055 title={Scikit-learn: Machine Learning in {P}ython},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1056 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1057 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1058 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1059 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1060 journal={Journal of Machine Learning Research},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1061 volume={12},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1062 pages={2825--2830},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1063 year={2011}
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1064 url = {https://github.com/scikit-learn/scikit-learn}
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
1065 }
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1066 </citation>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
1067 </citations>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
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1068 </xml>
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1069
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1070 <xml name="scipy_citation">
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1071 <citations>
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1072 <citation type="bibtex">
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1073 @Misc{,
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1074 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1075 title = {{SciPy}: Open source scientific tools for {Python}},
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1076 year = {2001--},
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1077 url = "http://www.scipy.org/",
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1078 note = {[Online; accessed 2016-04-09]}
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1079 }
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1080 </citation>
fe2d62fbf47b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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1081 </citations>
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1082 </xml>
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1083
6
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1084 </macros>