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annotate feature_selection.xml @ 9:537c6763c018 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
author bgruening
date Fri, 13 Jul 2018 03:55:31 -0400
parents b0d554b38770
children 96f9b73327f2
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@.1">
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2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$feature_selection_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="feature_selection_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import pickle
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22 import numpy as np
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23 import sklearn.feature_selection
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24 from sklearn import svm, linear_model, ensemble
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26 @COLUMNS_FUNCTION@
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28 @FEATURE_SELECTOR_FUNCTION@
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29
0
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30 input_json_path = sys.argv[1]
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31 with open(input_json_path, "r") as param_handler:
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32 params = json.load(param_handler)
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33
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34 ## Read features
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35 features_has_header = params["input_options"]["header1"]
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36 input_type = params["input_options"]["selected_input"]
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37 if input_type=="tabular":
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38 header = 'infer' if features_has_header else None
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39 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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40 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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41 c = params["input_options"]["column_selector_options_1"]["col1"]
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42 else:
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43 c = None
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44 X, input_df = read_columns(
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45 "$input_options.infile1",
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46 c = c,
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47 c_option = column_option,
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48 return_df = True,
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49 sep='\t',
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50 header=header,
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51 parse_dates=True
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52 )
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53 else:
9
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54 X = mmread("$input_options.infile1")
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55
2
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56 ## Read labels
0
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57 header = 'infer' if params["input_options"]["header2"] else None
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58 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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59 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
4
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60 c = params["input_options"]["column_selector_options_2"]["col2"]
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61 else:
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62 c = None
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63 y = read_columns(
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64 "$input_options.infile2",
4
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65 c = c,
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66 c_option = column_option,
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67 sep='\t',
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68 header=header,
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69 parse_dates=True
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70 )
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71 y=y.ravel()
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72
2
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73 ## Create feature selector
3
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74 new_selector = feature_selector(params['feature_selection_algorithms'])
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75 if params['feature_selection_algorithms']['selected_algorithm'] != 'SelectFromModel' or \
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76 'extra_estimator' not in params['feature_selection_algorithms'] or \
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77 params['feature_selection_algorithms']['extra_estimator']['has_estimator'] != 'no_load' :
2
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78 new_selector.fit(X, y)
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79
2
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80 ## Transform to select features
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81 selected_names = None
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82 if "$select_methods.selected_method" == "fit_transform":
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83 res = new_selector.transform(X)
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84 if features_has_header:
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85 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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86 else:
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87 res = new_selector.get_support(params["select_methods"]["indices"])
0
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88
2
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89 res = pandas.DataFrame(res, columns = selected_names)
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90 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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91
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92
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93 ]]>
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94 </configfile>
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bgruening
parents:
diff changeset
95 </configfiles>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
96 <inputs>
2
2eb90e73f0d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 0
diff changeset
97 <expand macro="feature_selection_all" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
98 <expand macro="feature_selection_methods" />
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
99 <expand macro="sl_mixed_input"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
100 </inputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
101 <outputs>
2
2eb90e73f0d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 0
diff changeset
102 <data format="tabular" name="outfile"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
103 </outputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
104 <tests>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
105 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
106 <param name="selected_algorithm" value="SelectFromModel"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
107 <param name="has_estimator" value="no"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
108 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
109 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
110 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
111 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
112 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
113 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
114 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
115 <output name="outfile" file="feature_selection_result01"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
116 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
117 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
118 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
119 <param name="param" value="20"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
120 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
121 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
122 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
123 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
124 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
125 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
126 <output name="outfile" file="feature_selection_result02"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
127 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
128 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
129 <param name="selected_algorithm" value="SelectPercentile"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
130 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
131 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
132 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
133 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
134 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
135 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
136 <output name="outfile" file="feature_selection_result03"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
137 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
138 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
139 <param name="selected_algorithm" value="SelectKBest"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
140 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
141 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
142 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
143 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
144 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
145 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
146 <output name="outfile" file="feature_selection_result04"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
147 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
148 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
149 <param name="selected_algorithm" value="SelectFpr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
150 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
151 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
152 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
153 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
154 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
155 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
156 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
157 <output name="outfile" file="feature_selection_result05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
158 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
159 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
160 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
161 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
162 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
163 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
164 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
165 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
166 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
167 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
168 <output name="outfile" file="feature_selection_result06"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
169 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
170 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
171 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
172 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
173 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
174 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
175 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
176 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
177 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
178 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
179 <output name="outfile" file="feature_selection_result07"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
180 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
181 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="selected_algorithm" value="RFE"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="has_estimator" value="no"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
188 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
189 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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190 <param name="header2" value="True"/>
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191 <output name="outfile" file="feature_selection_result08"/>
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192 </test>
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193 <test>
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194 <param name="selected_algorithm" value="RFECV"/>
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195 <param name="has_estimator" value="no"/>
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196 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
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197 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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198 <param name="header1" value="True"/>
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199 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
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200 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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201 <param name="col2" value="1"/>
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202 <param name="header2" value="True"/>
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203 <output name="outfile" file="feature_selection_result09"/>
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204 </test>
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205 <test>
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206 <param name="selected_algorithm" value="VarianceThreshold"/>
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207 <param name="threshold" value="0.1"/>
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208 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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209 <param name="header1" value="True"/>
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210 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
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211 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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212 <param name="col2" value="1"/>
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213 <param name="header2" value="True"/>
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214 <output name="outfile" file="feature_selection_result10"/>
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215 </test>
6
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216 <test>
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217 <param name="selected_algorithm" value="SelectKBest"/>
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218 <param name="k" value="3"/>
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219 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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220 <param name="header1" value="True"/>
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221 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
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222 <param name="col1" value="target"/>
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223 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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224 <param name="header2" value="True"/>
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225 <param name="selected_column_selector_option2" value="by_header_name"/>
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226 <param name="col2" value="target"/>
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227 <output name="outfile" file="feature_selection_result11"/>
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228 </test>
0
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229 </tests>
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230 <help>
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231 <![CDATA[
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232 **What it does**
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233 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on
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234 sklearn.metrics package.
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235 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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236
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237 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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238 ]]>
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239 </help>
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240 <expand macro="sklearn_citation"/>
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241 </tool>