sklearn_model_validation: model_validation.xml annotate

annotate model_validation.xml @ 2:eb4a0fccbb3f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978

author	bgruening
date	Wed, 30 May 2018 08:23:35 -0400
parents	1e778f5614bf
children	2e4d425cd108

rev	line source
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	1 <tool id="sklearn_model_validation" name="Model Validation" version="@VERSION@">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	2 <description>evaluates estimator performance by cross-validation</description>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	3 <macros>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	4 <import>main_macros.xml</import>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	5 </macros>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	6 <expand macro="python_requirements"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	7 <expand macro="macro_stdio"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	8 <version_command>echo "@VERSION@"</version_command>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	9 <command>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	10 <![CDATA[
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	11 python "$sklearn_model_validation_script" '$inputs'
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	12 ]]>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	13 </command>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	14 <configfiles>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	15 <inputs name="inputs" />
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	16 <configfile name="sklearn_model_validation_script">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	17 <![CDATA[
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	18 import sys
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	19 import json
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	20 import pandas
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	21 import ast
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	22 import pickle
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	23 import numpy as np
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	24 import sklearn.model_selection
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	25 from sklearn import svm, linear_model, ensemble
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	26 from sklearn.pipeline import Pipeline
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	27
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	28 @COLUMNS_FUNCTION@
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	29
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	30 @FEATURE_SELECTOR_FUNCTION@
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	31
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	32 input_json_path = sys.argv[1]
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	33 params = json.load(open(input_json_path, "r"))
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	34
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	35 input_type = params["input_options"]["selected_input"]
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	36 if input_type=="tabular":
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	37 header = 'infer' if params["input_options"]["header1"] else None
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	38 X = read_columns(
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	39 "$input_options.infile1",
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	40 "$input_options.col1",
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	41 sep='\t',
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	42 header=header,
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	43 parse_dates=True
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	44 )
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	45 else:
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	46 X = mmread(open("$input_options.infile1", 'r'))
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	47
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	48 header = 'infer' if params["input_options"]["header2"] else None
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	49 y = read_columns(
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	50 "$input_options.infile2",
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	51 "$input_options.col2",
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	52 sep='\t',
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	53 header=header,
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	54 parse_dates=True
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	55 )
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	56 y=y.ravel()
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	57
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	58 options = params["model_validation_functions"]["options"]
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	59 if 'scoring' in options and options['scoring'] == '':
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	60 options['scoring'] = None
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	61 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	62 options['pre_dispatch'] = None
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	63
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	64 pipeline_steps = []
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	65
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	66 ## Set up feature selector and add to pipeline steps.
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	67 if params['feature_selection']['do_feature_selection'] == 'Yes':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	68 feature_selector = feature_selector(params['feature_selection']['feature_selection_algorithms'])
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	69 pipeline_steps.append( ('feature_selector', feature_selector))
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	70
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	71 ## Set up estimator and add to pipeline.
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	72 estimator=params["model_validation_functions"]["estimator"]
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	73 if params["model_validation_functions"]["extra_estimator"]["has_estimator"] == 'no':
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	74 estimator = params["model_validation_functions"]["extra_estimator"]["new_estimator"]
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	75 estimator = eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	76
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	77 pipeline_steps.append( ('estimator', estimator) )
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	78
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	79 pipeline = Pipeline(pipeline_steps)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	80
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	81 ## Set up validator, run pipeline through validator and return results.
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	82
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	83 validator = params["model_validation_functions"]["selected_function"]
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	84 validator = getattr(sklearn.model_selection, validator)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	85
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	86 selected_function = params["model_validation_functions"]["selected_function"]
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	87 rval_type = params["model_validation_functions"].get("return_type", None)
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	88
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	89 if selected_function == 'cross_validate':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	90 res = validator(pipeline, X, y, **options)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	91 rval = res[rval_type]
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	92 elif selected_function == 'learning_curve':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	93 options['train_sizes'] = eval(options['train_sizes'])
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	94 train_sizes_abs, train_scores, test_scores = validator(pipeline, X, y, **options)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	95 rval = eval(rval_type)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	96 elif selected_function == 'permutation_test_score':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	97 score, permutation_scores, pvalue = validator(pipeline, X, y, **options)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	98 rval = eval(rval_type)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	99 if rval_type in ["score", "pvalue"]:
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	100 rval = [rval]
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	101 elif selected_function == 'validation_curve':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	102 options['param_name'] = 'estimator__' + options['param_name']
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	103 options['param_range'] = eval(options['param_range'])
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	104 train_scores, test_scores = validator(pipeline, X, y, **options)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	105 rval = eval(rval_type)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	106 elif selected_function == 'GridSearchCV':
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	107 param_grid = params["model_validation_functions"]["param_grid"].replace("__sq__","'")\
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	108 .replace('__dq__','"').replace("__oc__", "{").replace("__cc__", "}")\
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	109 .replace("__ob__", "[").replace("__cb__", "]")
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	110 param_grid = ast.literal_eval(param_grid)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	111 grid = validator(pipeline, param_grid, **options)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	112 grid.fit(X, y)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	113 rval = getattr(grid, rval_type)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	114 if rval_type in ["best_estimator_", "best_score_", "best_index_"]:
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	115 rval = [rval]
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	116 else:
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	117 rval = validator(pipeline, X, y, **options)
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	118
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	119 rval = pandas.DataFrame(rval)
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	120 if rval_type and rval_type == "cv_results_":
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	121 rval.to_csv(path_or_buf="$outfile", sep='\t', header=True, index=False)
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	122 else:
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	123 rval.to_csv(path_or_buf="$outfile", sep='\t', header=False, index=False)
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	124
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	125 ]]>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	126 </configfile>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	127 </configfiles>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	128 <inputs>
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	129 <conditional name="feature_selection">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	130 <param name="do_feature_selection" type="select" label="Do feature selection?">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	131 <option value="No" selected="true"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	132 <option value="Yes"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	133 </param>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	134 <when value="No"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	135 <when value="Yes">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	136 <expand macro="feature_selection_all"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	137 </when>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	138 </conditional>
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	139 <conditional name="model_validation_functions">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	140 <param name="selected_function" type="select" label="Select a model validation function">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	141 <option value="GridSearchCV">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option>
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	142 <option value="cross_validate">cross_validate - Evaluate metric(s) by cross-validation and also record fit/score times</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	143 <option value="cross_val_predict">cross_val_predict - Generate cross-validated estimates for each input data point</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	144 <option value="cross_val_score">cross_val_score - Evaluate a score by cross-validation</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	145 <option value="learning_curve">learning_curve - Learning curve</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	146 <option value="permutation_test_score">permutation_test_score - Evaluate the significance of a cross-validated score with permutations</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	147 <option value="validation_curve">validation_curve - Validation curve</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	148 </param>
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	149 <when value="GridSearchCV">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	150 <expand macro="estimator_input_no_fit" />
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	151 <param argument="param_grid" type="text" value="[{'feature_selector__k': [3, 5, 7, 9], 'estimator__C': [1, 10, 100, 1000]}]" label="param_grid" help="Dictionary with parameters names (string) as keys and lists of parameter settings to try as values, or a list of such dictionaries, in which case the grids spanned by each dictionary in the list are explored"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	152 <section name="options" title="Other Options" expanded="false">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	153 <expand macro="scoring"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	154 <expand macro="model_validation_common_options"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	155 <expand macro="pre_dispatch" value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	156 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="Data is identically distributed?"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	157 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset."/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	158 <!--error_score-->
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	159 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	160 </section>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	161 <param name="return_type" type="select" label="Select a return type">
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	162 <option value="cv_results_" selected="true">cv_results_</option>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	163 <option value="best_estimator_">best_estimator_</option>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	164 <option value="best_score_">best_score_</option>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	165 <option value="best_params_">best_params_</option>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	166 <option value="best_index_">best_index_</option>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	167 </param>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	168 </when>
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	169 <when value="cross_validate">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	170 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	171 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	172 <!--groups-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	173 <expand macro="model_validation_common_options"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	174 <expand macro="scoring"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	175 <!--fit_params-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	176 <expand macro="pre_dispatch"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	177 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	178 <param name="return_type" type="select" label="Select a return type">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	179 <option value="test_score" selected="true">test_score</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	180 <option value="train_score">train_score</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	181 <option value="fit_time">fit_time</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	182 <option value="score_time">score_time</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	183 </param>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	184 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	185 <when value="cross_val_predict">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	186 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	187 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	188 <!--groups-->
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	189 <expand macro="model_validation_common_options" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	190 <!--fit_params-->
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	191 <expand macro="pre_dispatch" value="2*n_jobs’" help="Controls the number of jobs that get dispatched during parallel execution"/>
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	192 <param argument="method" type="select" label="Invokes the passed method name of the passed estimator">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	193 <option value="predict" selected="true">predict</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	194 <option value="predict_proba">predict_proba</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	195 </param>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	196 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	197 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	198 <when value="cross_val_score">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	199 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	200 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	201 <!--groups-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	202 <expand macro="model_validation_common_options"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	203 <expand macro="scoring"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	204 <!--fit_params-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	205 <expand macro="pre_dispatch"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	206 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	207 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	208 <when value="learning_curve">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	209 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	210 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	211 <!--groups-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	212 <expand macro="model_validation_common_options"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	213 <param argument="train_sizes" type="text" value="np.linspace(0.1, 1.0, 5)" label="train_sizes" help="Relative or absolute numbers of training examples that will be used to generate the learning curve"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	214 <expand macro="scoring"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	215 <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="exploit_incremental_learning" help="Whether to apply incremental learning to speed up fitting of the estimator if supported"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	216 <expand macro="pre_dispatch"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	217 <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	218 <expand macro="random_state"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	219 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	220 <param name="return_type" type="select" label="Select a return type">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	221 <option value="train_sizes_abs" selected="true">train_sizes_abs</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	222 <option value="train_scores">train_scores</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	223 <option value="test_scores">test_scores</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	224 </param>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	225 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	226 <when value="permutation_test_score">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	227 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	228 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	229 <!--groups-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	230 <expand macro="model_validation_common_options"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	231 <expand macro="scoring"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	232 <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	233 <expand macro="random_state"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	234 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	235 <param name="return_type" type="select" label="Select a return type">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	236 <option value="score" selected="true">score</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	237 <option value="permutation_scores">permutation_scores</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	238 <option value="pvalue">pvalue</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	239 </param>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	240 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	241 <when value="validation_curve">
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	242 <expand macro="estimator_input_no_fit" />
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	243 <section name="options" title="Other Options" expanded="false">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	244 <param name="param_name" type="text" value="gamma" label="param_name" help="Name of the parameter that will be varied"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	245 <param name="param_range" type="text" value="np.logspace(-6, -1, 5)" label="param_range" help="The values of the parameter that will be evaluated."/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	246 <!--groups-->
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	247 <expand macro="model_validation_common_options"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	248 <expand macro="scoring"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	249 <expand macro="pre_dispatch"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	250 </section>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	251 <param name="return_type" type="select" label="Select a return type">
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	252 <option value="train_scores" selected="true">train_scores</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	253 <option value="test_scores">test_scores</option>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	254 </param>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	255 </when>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	256 </conditional>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	257 <expand macro="sl_mixed_input"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	258 </inputs>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	259 <outputs>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	260 <data format="tabular" name="outfile"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	261 </outputs>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	262 <tests>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	263 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	264 <param name="selected_function" value="cross_validate"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	265 <param name="estimator" value="linear_model.LassoCV()"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	266 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	267 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	268 <param name="col1" value="1,2,3,4,5"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	269 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	270 <param name="col2" value="6"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	271 <output name="outfile" file="mv_result01.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	272 </test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	273 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	274 <param name="selected_function" value="cross_val_predict"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	275 <param name="estimator" value="linear_model.LassoCV()"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	276 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	277 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	278 <param name="col1" value="1,2,3,4,5"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	279 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	280 <param name="col2" value="6"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	281 <output name="outfile" file="mv_result02.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	282 </test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	283 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	284 <param name="selected_function" value="cross_val_score"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	285 <param name="estimator" value="linear_model.LassoCV()"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	286 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	287 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	288 <param name="col1" value="1,2,3,4,5"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	289 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	290 <param name="col2" value="6"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	291 <output name="outfile" file="mv_result03.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	292 </test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	293 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	294 <param name="selected_function" value="learning_curve"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	295 <param name="estimator" value="linear_model.LassoCV()"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	296 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	297 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	298 <param name="header1" value="true" />
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	299 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	300 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	301 <param name="header2" value="true" />
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	302 <param name="col2" value="1"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	303 <output name="outfile" file="mv_result04.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	304 </test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	305 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	306 <param name="selected_function" value="permutation_test_score"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	307 <param name="estimator" value="linear_model.LassoCV()"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	308 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	309 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	310 <param name="col1" value="1,2,3,4,5"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	311 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	312 <param name="col2" value="6"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	313 <output name="outfile" file="mv_result05.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	314 </test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	315 <test>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	316 <param name="selected_function" value="validation_curve"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	317 <param name="estimator" value="svm.SVC(kernel="linear")"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	318 <param name="has_estimator" value="yes"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	319 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	320 <param name="header1" value="true" />
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	321 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	322 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	323 <param name="header2" value="true" />
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	324 <param name="col2" value="1"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	325 <param name="return_type" value="test_scores"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	326 <output name="outfile" file="mv_result06.tabular"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	327 </test>
2 eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	328 <test>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	329 <param name="do_feature_selection" value="Yes"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	330 <param name="selected_algorithm" value="SelectKBest"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	331 <param name="score_func" value="chi2"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	332 <param name="selected_function" value="GridSearchCV"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	333 <param name="estimator" value="svm.SVR(kernel="linear")"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	334 <param name="has_estimator" value="yes"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	335 <param name="param_grid" value="[{'feature_selector__k': [3, 7], 'estimator__C': [1, 100]}]"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	336 <param name="return_type" value="best_score_"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	337 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	338 <param name="header1" value="true" />
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	339 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	340 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	341 <param name="header2" value="true" />
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	342 <param name="col2" value="1"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	343 <output name="outfile" file="mv_result07.tabular"/>
eb4a0fccbb3f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978 bgruening parents: 0 diff changeset	344 </test>
0 1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	345 </tests>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	346 <help>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	347 <![CDATA[
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	348 What it does
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	349 This tool includes model validation functions to evaluate estimator performance in the cross-validation approach. This tool is based on
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	350 sklearn.model_selection package.
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	351 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	352
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	353 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	354 ]]>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	355 </help>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	356 <expand macro="sklearn_citation"/>
1e778f5614bf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee bgruening parents: diff changeset	357 </tool>

Mercurial > repos > bgruening > sklearn_model_validation

annotate model_validation.xml @ 2:eb4a0fccbb3f draft