Mercurial > repos > bgruening > sklearn_feature_selection
annotate feature_selection.xml @ 25:41b109e70a7f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author | bgruening |
---|---|
date | Mon, 16 Dec 2019 05:30:39 -0500 |
parents | c2cd3219543a |
children | 93f3b307485f |
rev | line source |
---|---|
20
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@"> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
3 <macros> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
4 <import>main_macros.xml</import> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
5 </macros> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
6 <expand macro="python_requirements"/> |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
7 <!--TODO: Add imblearn package support--> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
8 <expand macro="macro_stdio"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
9 <version_command>echo "@VERSION@"</version_command> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
10 <command> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
11 <![CDATA[ |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
12 python "$feature_selection_script" '$inputs' |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
13 ]]> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
14 </command> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
15 <configfiles> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
16 <inputs name="inputs" /> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
17 <configfile name="feature_selection_script"> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
18 <![CDATA[ |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
19 import json |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
20 import sklearn.feature_selection |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
21 import skrebate |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
22 import pandas |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
23 import sys |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
24 import warnings |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
25 import xgboost |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
26 from sklearn import ( |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
27 cluster, compose, decomposition, ensemble, feature_extraction, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
28 feature_selection, gaussian_process, kernel_approximation, metrics, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
29 model_selection, naive_bayes, neighbors, pipeline, preprocessing, |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
30 svm, linear_model, tree, discriminant_analysis) |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
31 from imblearn.pipeline import Pipeline as imbPipeline |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
32 from sklearn.pipeline import Pipeline |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
33 |
20
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
34 from galaxy_ml.utils import (SafeEval, feature_selector, |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
35 read_columns, get_module) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
36 |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
37 |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
38 warnings.simplefilter('ignore') |
13
f8dfdb47508b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
10
diff
changeset
|
39 |
f8dfdb47508b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
10
diff
changeset
|
40 safe_eval = SafeEval() |
3
3a1acc39b39b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents:
2
diff
changeset
|
41 |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
42 input_json_path = sys.argv[1] |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
43 with open(input_json_path, 'r') as param_handler: |
9
537c6763c018
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents:
6
diff
changeset
|
44 params = json.load(param_handler) |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
45 |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
46 ## handle cheetah |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
47 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\ |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
48 and $fs_algorithm_selector.model_inputter.input_mode == 'prefitted': |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
49 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\ |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
50 '$fs_algorithm_selector.model_inputter.fitted_estimator' |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
51 #end if |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
52 |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
53 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\ |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
54 and $fs_algorithm_selector.model_inputter.input_mode == 'new'\ |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
55 and $fs_algorithm_selector.model_inputter.estimator_selector.selected_module == 'custom_estimator': |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
56 params['fs_algorithm_selector']['model_inputter']['estimator_selector']['c_estimator'] =\ |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
57 '$fs_algorithm_selector.model_inputter.estimator_selector.c_estimator' |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
58 #end if |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
59 |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
60 #if $fs_algorithm_selector.selected_algorithm in ['RFE', 'RFECV', 'DyRFECV']\ |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
61 and $fs_algorithm_selector.estimator_selector.selected_module == 'custom_estimator': |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
62 params['fs_algorithm_selector']['estimator_selector']['c_estimator'] =\ |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
63 '$fs_algorithm_selector.estimator_selector.c_estimator' |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
64 #end if |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
65 |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
66 #if $fs_algorithm_selector.selected_algorithm in ['RFECV', 'DyRFECV']\ |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
67 and $fs_algorithm_selector.options.cv_selector.selected_cv\ |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
68 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']: |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
69 params['fs_algorithm_selector']['options']['cv_selector']['groups_selector']['infile_g'] =\ |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
70 '$fs_algorithm_selector.options.cv_selector.groups_selector.infile_g' |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
71 #end if |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
72 |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
73 ## Read features |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
74 features_has_header = params['input_options']['header1'] |
20
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
75 #if $input_options.selected_input == 'tabular' |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
76 header = 'infer' if features_has_header else None |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
77 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option'] |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
78 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']: |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
79 c = params['input_options']['column_selector_options_1']['col1'] |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
80 else: |
20
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
81 c = None |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
82 X, input_df = read_columns( |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
83 '$input_options.infile1', |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
84 c = c, |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
85 c_option = column_option, |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
86 return_df = True, |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
87 sep='\t', |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
88 header=header, |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
89 parse_dates=True) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
90 X = X.astype(float) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
91 #elif $input_options.selected_input == 'seq_fasta' |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
92 fasta_file = '$input_options.fasta_file' |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
93 pyfaidx = get_module('pyfaidx') |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
94 sequences = pyfaidx.Fasta(fasta_file) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
95 n_seqs = len(sequences.keys()) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
96 X = np.arange(n_seqs)[:, np.newaxis] |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
97 for param in estimator_params.keys(): |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
98 if param.endswith('fasta_path'): |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
99 estimator.set_params( |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
100 **{param: fasta_file}) |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
101 else: |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
102 raise ValueError( |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
103 "The selected estimator doesn't support " |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
104 "fasta file input! Please consider using " |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
105 "KerasGBatchClassifier with " |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
106 "FastaDNABatchGenerator/FastaProteinBatchGenerator " |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
107 "or having GenomeOneHotEncoder/ProteinOneHotEncoder " |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
108 "in pipeline!") |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
109 #elif $input_options.selected_input == 'sparse' |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
110 X = mmread('$input_options.infile1') |
0b88494bdcac
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
18
diff
changeset
|
111 #end if |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
112 |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
113 ## Read labels |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
114 header = 'infer' if params['input_options']['header2'] else None |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
115 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2'] |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
116 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']: |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
117 c = params['input_options']['column_selector_options_2']['col2'] |
4
44e26f8a82c6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents:
3
diff
changeset
|
118 else: |
44e26f8a82c6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents:
3
diff
changeset
|
119 c = None |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
120 y = read_columns( |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
121 '$input_options.infile2', |
4
44e26f8a82c6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents:
3
diff
changeset
|
122 c = c, |
44e26f8a82c6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents:
3
diff
changeset
|
123 c_option = column_option, |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
124 sep='\t', |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
125 header=header, |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
126 parse_dates=True) |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
127 y = y.ravel() |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
128 |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
129 ## Create feature selector |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
130 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y) |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
131 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\ |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
132 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' : |
2
2eb90e73f0d5
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents:
0
diff
changeset
|
133 new_selector.fit(X, y) |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
134 |
2
2eb90e73f0d5
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents:
0
diff
changeset
|
135 ## Transform to select features |
2eb90e73f0d5
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents:
0
diff
changeset
|
136 selected_names = None |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
137 |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
138 res = new_selector.transform(X) |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
139 if features_has_header: |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
140 selected_names = input_df.columns[new_selector.get_support(indices=True)] |
2
2eb90e73f0d5
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents:
0
diff
changeset
|
141 res = pandas.DataFrame(res, columns = selected_names) |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
142 res.to_csv(path_or_buf='$outfile', sep='\t', index=False) |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
143 |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
144 #if $save: |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
145 with open('$outfile_selector', 'wb') as output_handler: |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
146 pickle.dump(new_selector, output_handler, pickle.HIGHEST_PROTOCOL) |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
147 #end if |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
148 |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
149 ]]> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
150 </configfile> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
151 </configfiles> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
152 <inputs> |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
153 <expand macro="feature_selection_fs"/> |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
154 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?"/> |
22
c2cd3219543a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents:
20
diff
changeset
|
155 <expand macro="sl_mixed_input_plus_sequence"/> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
156 </inputs> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
157 <outputs> |
17
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
158 <data format="tabular" name="outfile" /> |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
159 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}"> |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
160 <filter>save</filter> |
2bbbac61e48d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
15
diff
changeset
|
161 </data> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
162 </outputs> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
163 <tests> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
164 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
165 <param name="selected_algorithm" value="SelectFromModel"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
166 <param name="input_mode" value="new"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
167 <param name="selected_module" value="ensemble"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
168 <param name="selected_estimator" value="RandomForestRegressor"/> |
13
f8dfdb47508b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
10
diff
changeset
|
169 <param name="text_params" value="n_estimators=10, random_state=10"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
170 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
171 <param name="header1" value="false"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
172 <param name="col1" value="1,2,3,4,5"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
173 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
174 <param name="col2" value="6"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
175 <param name="header2" value="false"/> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
176 <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
|
177 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
178 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
179 <param name="selected_algorithm" value="GenericUnivariateSelect"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
180 <param name="param" value="20"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
181 <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
|
182 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
183 <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
|
184 <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
|
185 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
186 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
187 <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
|
188 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
189 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
190 <param name="selected_algorithm" value="SelectPercentile"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
191 <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
|
192 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
193 <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
|
194 <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
|
195 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
196 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
197 <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
|
198 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
199 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
200 <param name="selected_algorithm" value="SelectKBest"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
201 <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
|
202 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
203 <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
|
204 <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
|
205 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
206 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
207 <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
|
208 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
209 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
210 <param name="selected_algorithm" value="SelectFpr"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
211 <param name="alpha" value="0.05"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
212 <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
|
213 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
214 <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
|
215 <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
|
216 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
217 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
218 <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
|
219 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
220 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
221 <param name="selected_algorithm" value="SelectFdr"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
222 <param name="alpha" value="0.05"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
223 <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
|
224 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
225 <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
|
226 <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
|
227 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
228 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
229 <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
|
230 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
231 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
232 <param name="selected_algorithm" value="SelectFwe"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
233 <param name="alpha" value="0.05"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
234 <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
|
235 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
236 <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
|
237 <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
|
238 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
239 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
240 <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
|
241 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
242 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
243 <param name="selected_algorithm" value="RFE"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
244 <param name="input_mode" value="new"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
245 <param name="selected_module" value="ensemble"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
246 <param name="selected_estimator" value="RandomForestRegressor"/> |
13
f8dfdb47508b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
10
diff
changeset
|
247 <param name="text_params" value="n_estimators=10, random_state=10"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
248 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
249 <param name="header1" value="false"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
250 <param name="col1" value="1,2,3,4,5"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
251 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
252 <param name="col2" value="6"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
253 <param name="header2" value="false"/> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
254 <output name="outfile" file="feature_selection_result08"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
255 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
256 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
257 <param name="selected_algorithm" value="RFECV"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
258 <param name="input_mode" value="new"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
259 <param name="selected_module" value="ensemble"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
260 <param name="selected_estimator" value="RandomForestRegressor"/> |
13
f8dfdb47508b
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
10
diff
changeset
|
261 <param name="text_params" value="n_estimators=10, random_state=10"/> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
262 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
263 <param name="header1" value="false"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
264 <param name="col1" value="1,2,3,4,5"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
265 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
266 <param name="col2" value="6"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
267 <param name="header2" value="false"/> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
268 <output name="outfile" file="feature_selection_result09"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
269 </test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
270 <test> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
271 <param name="selected_algorithm" value="VarianceThreshold"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
272 <param name="threshold" value="0.1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
273 <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
|
274 <param name="header1" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
275 <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
|
276 <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
|
277 <param name="col2" value="1"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
278 <param name="header2" value="True"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
279 <output name="outfile" file="feature_selection_result10"/> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
280 </test> |
6
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
281 <test> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
282 <param name="selected_algorithm" value="SelectKBest"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
283 <param name="k" value="3"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
284 <param name="infile1" value="test3.tabular" ftype="tabular"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
285 <param name="header1" value="True"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
286 <param name="selected_column_selector_option" value="all_but_by_header_name"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
287 <param name="col1" value="target"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
288 <param name="infile2" value="test3.tabular" ftype="tabular"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
289 <param name="header2" value="True"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
290 <param name="selected_column_selector_option2" value="by_header_name"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
291 <param name="col2" value="target"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
292 <output name="outfile" file="feature_selection_result11"/> |
b0d554b38770
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents:
5
diff
changeset
|
293 </test> |
10
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
294 <test> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
295 <param name="selected_algorithm" value="SelectFromModel"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
296 <param name="input_mode" value="prefitted"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
297 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
298 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
299 <param name="header1" value="false"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
300 <param name="col1" value="1,2,3,4,5"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
301 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
302 <param name="col2" value="1"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
303 <param name="header2" value="false"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
304 <output name="outfile" file="feature_selection_result12"/> |
96f9b73327f2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents:
9
diff
changeset
|
305 </test> |
18
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
306 <test> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
307 <param name="selected_algorithm" value="RFECV"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
308 <param name="input_mode" value="new"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
309 <param name="selected_module" value="ensemble"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
310 <param name="selected_estimator" value="RandomForestRegressor"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
311 <param name="text_params" value="n_estimators=10, random_state=10"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
312 <section name="groups_selector"> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
313 <param name="infile_groups" value="regression_y.tabular" ftype="tabular"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
314 <param name="header_g" value="true"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
315 <param name="selected_column_selector_option_g" value="by_index_number"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
316 <param name="col_g" value="1"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
317 </section> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
318 <param name="selected_cv" value="GroupShuffleSplit"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
319 <param name="random_state" value="0"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
320 <param name="infile1" value="regression_X.tabular" ftype="tabular"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
321 <param name="header1" value="true"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
322 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
323 <param name="infile2" value="regression_y.tabular" ftype="tabular"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
324 <param name="col2" value="1"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
325 <param name="header2" value="true"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
326 <output name="outfile" file="feature_selection_result13"/> |
ec25331946b8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
17
diff
changeset
|
327 </test> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
328 </tests> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
329 <help> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
330 <![CDATA[ |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
331 **What it does** |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
332 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 |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
333 sklearn.metrics package. |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
334 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_. |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
335 |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
336 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
337 ]]> |
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
338 </help> |
14
dc411a215138
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
13
diff
changeset
|
339 <expand macro="sklearn_citation"> |
dc411a215138
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
13
diff
changeset
|
340 <expand macro="skrebate_citation"/> |
dc411a215138
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
13
diff
changeset
|
341 <expand macro="xgboost_citation"/> |
dc411a215138
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents:
13
diff
changeset
|
342 </expand> |
0
092199a095dd
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff
changeset
|
343 </tool> |