sklearn_feature_selection: feature_selection.xml annotate

annotate feature_selection.xml @ 22:c2cd3219543a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"

author	bgruening
date	Wed, 02 Oct 2019 04:05:05 -0400
parents	0b88494bdcac
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>

Mercurial > repos > bgruening > sklearn_feature_selection

annotate feature_selection.xml @ 22:c2cd3219543a draft