Mercurial > repos > bgruening > sklearn_generalized_linear

annotate generalized_linear.xml @ 34:b9a8876452cf draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 15:54:08 +0000
parents 4b49bade2949
children a8771df897b2
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1 <tool id="sklearn_generalized_linear" name="Generalized linear models" version="@VERSION@" profile="20.05">
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2 <description>for classification and regression</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements" />
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7 <expand macro="macro_stdio" />
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command><![CDATA[
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10 python "$glm_script" '$inputs'
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11 ]]>
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12 </command>
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13 <configfiles>
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14 <inputs name="inputs" />
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15 <configfile name="glm_script"><![CDATA[
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16 import sys
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17 import json
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18 import numpy as np
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19 import sklearn.linear_model
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20 import pandas
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21 import pickle
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22
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23 from scipy.io import mmread
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24 from galaxy_ml.utils import load_model, get_X_y
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27 input_json_path = sys.argv[1]
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28 with open(input_json_path, "r") as param_handler:
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29 params = json.load(param_handler)
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31 #if $selected_tasks.selected_task == "train":
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33 X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2")
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35 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
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36 options = params["selected_tasks"]["selected_algorithms"]["options"]
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38 my_class = getattr(sklearn.linear_model, algorithm)
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39 estimator = my_class(**options)
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40 estimator.fit(X,y)
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41 with open("$outfile_fit", 'wb') as out_handler:
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42 pickle.dump(estimator, out_handler, pickle.HIGHEST_PROTOCOL)
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44 #else:
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45 with open("$selected_tasks.infile_model", 'rb') as model_handler:
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46 classifier_object = load_model(model_handler)
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47 header = 'infer' if params["selected_tasks"]["header"] else None
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48 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
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49 prediction = classifier_object.predict(data)
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50 prediction_df = pandas.DataFrame(prediction, columns=["predicted"])
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51 res = pandas.concat([data, prediction_df], axis=1)
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52 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False, header=None)
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53 #end if
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55 ]]>
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56 </configfile>
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57 </configfiles>
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58 <inputs>
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59 <expand macro="sl_Conditional" model="zip">
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60 <param name="selected_algorithm" type="select" label="Select a linear model:">
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61 <option value="SGDClassifier" selected="true">Stochastic Gradient Descent (SGD) classifier</option>
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62 <option value="SGDRegressor">Stochastic Gradient Descent (SGD) regressor</option>
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63 <option value="LinearRegression">Linear Regression model</option>
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64 <option value="RidgeClassifier">Ridge classifier</option>
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65 <option value="Ridge">Ridge regressor</option>
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66 <option value="LogisticRegression">Logistic Regression</option>
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67 <option value="LogisticRegressionCV">Logitic Regression with Cross Validation</option>
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68 <option value="Perceptron">Perceptron</option>
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69 </param>
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70 <when value="SGDClassifier">
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71 <expand macro="sl_mixed_input" />
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72 <section name="options" title="Advanced Options" expanded="False">
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73 <expand macro="loss">
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74 <option value="hinge" selected="true">hinge</option>
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75 <option value="log">log</option>
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76 <option value="modified_huber">modified huber</option>
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77 <option value="squared_hinge">squared hinge</option>
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78 <option value="perceptron">perceptron</option>
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79 </expand>
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80 <expand macro="penalty" />
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81 <expand macro="alpha" />
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82 <expand macro="l1_ratio" />
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83 <expand macro="fit_intercept" />
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84 <expand macro="n_iter_no_change" />
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85 <expand macro="shuffle" />
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86 <expand macro="epsilon" />
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87 <expand macro="learning_rate_s" selected1="true" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
88 <expand macro="eta0" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
89 <expand macro="power_t" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
90 <!--class_weight-->
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
91 <expand macro="warm_start" checked="false" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
92 <expand macro="random_state" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
93 <!--average-->
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
94 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
95 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
96 <when value="SGDRegressor">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
97 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
98 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
99 <expand macro="loss" select="true" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
100 <expand macro="penalty" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
101 <expand macro="alpha" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
102 <expand macro="l1_ratio" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
103 <expand macro="fit_intercept" />
31
4b49bade2949 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 28
diff changeset
104 <expand macro="n_iter_no_change" />
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
105 <expand macro="shuffle" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
106 <expand macro="epsilon" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
107 <expand macro="learning_rate_s" selected2="true" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
108 <expand macro="eta0" default_value="0.01" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
109 <expand macro="power_t" default_value="0.25" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
110 <expand macro="warm_start" checked="false" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
111 <expand macro="random_state" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
112 <!--average-->
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
113 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
114 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
115 <when value="LinearRegression">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
116 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
117 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
118 <expand macro="fit_intercept" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
119 <expand macro="normalize" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
120 <expand macro="copy_X" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
121 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
122 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
123 <when value="RidgeClassifier">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
124 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
125 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
126 <expand macro="ridge_params" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
127 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
128 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
129 <when value="Ridge">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
130 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
131 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
132 <expand macro="ridge_params" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
133 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
134 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
135 <when value="LogisticRegression">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
136 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
137 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
138 <expand macro="penalty" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
139 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
140 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
141 <expand macro="C" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
142 <expand macro="fit_intercept" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
143 <expand macro="max_iter" default_value="100" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
144 <expand macro="warm_start" checked="false" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
145 <param argument="solver" type="select" label="Optimization algorithm" help=" ">
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
146 <option value="liblinear" selected="true">liblinear</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
147 <option value="sag">sag</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
148 <option value="lbfgs">lbfgs</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
149 <option value="newton-cg">newton-cg</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
150 </param>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
151 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. " />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
152 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. ">
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
153 <option value="ovr" selected="true">ovr</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
154 <option value="multinomial">multinomial</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
155 </param>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
156 <!--class_weight-->
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
157 <expand macro="random_state" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
158 </section>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
159 </when>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
160 <when value="LogisticRegressionCV">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
161 <expand macro="sl_mixed_input" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
162 <section name="options" title="Advanced Options" expanded="False">
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
163 <param argument="Cs" type="integer" value="10" label="Inverse of regularization strength" help="A grid of Cs values are chosen in a logarithmic scale between 1e-4 and 1e4. Like in support vector machines, smaller values specify stronger regularization. " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
164 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
165 <param argument="cv" type="integer" optional="true" value="" label="Number of folds used in cross validation" help="If not set, the default cross-validation generator (Stratified K-Folds) is used. " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
166 <expand macro="penalty" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
167 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
168 <expand macro="fit_intercept" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
169 <expand macro="max_iter" default_value="100" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
170 <param argument="solver" type="select" label="Optimization algorithm" help=" ">
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
171 <option value="liblinear" selected="true">liblinear</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
172 <option value="sag">sag</option>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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173 <option value="lbfgs">lbfgs</option>
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174 <option value="newton-cg">newton-cg</option>
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175 </param>
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176 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. " />
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177 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. ">
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178 <option value="ovr" selected="true">ovr</option>
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179 <option value="multinomial">multinomial</option>
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180 </param>
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181 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Average scores across all folds" help=" " />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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182 <expand macro="random_state" />
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183 <!--scoring=None> <class_weight=None-->
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184 </section>
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185 </when>
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186 <when value="Perceptron">
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187 <expand macro="sl_mixed_input" />
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188 <section name="options" title="Advanced Options" expanded="False">
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189 <expand macro="penalty" default_value="none" />
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190 <expand macro="alpha" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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191 <expand macro="fit_intercept" />
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192 <expand macro="n_iter_no_change" />
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193 <expand macro="shuffle" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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194 <expand macro="eta0" default_value="1" />
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195 <expand macro="warm_start" checked="false" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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196 <expand macro="random_state" default_value="0" />
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197 <!--class_weight=None-->
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198 </section>
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199 </when>
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200 </expand>
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201 </inputs>
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202 <expand macro="output" />
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203 <tests>
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204 <test>
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205 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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206 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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207 <param name="selected_column_selector_option" value="all_but_by_index_number" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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208 <param name="col1" value="6" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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209 <param name="col2" value="6" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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210 <param name="selected_task" value="train" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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211 <param name="selected_algorithm" value="SGDRegressor" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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212 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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213 <output name="outfile_fit" file="glm_model01" compare="sim_size" delta="5" />
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214 </test>
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215 <test>
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216 <param name="infile_model" value="glm_model01" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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217 <param name="infile_data" value="regression_test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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218 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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219 <output name="outfile_predict" file="glm_result01" lines_diff="4" />
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6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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220 </test>
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221 <test>
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b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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222 <param name="infile1" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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223 <param name="infile2" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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224 <param name="col1" value="1,2,3,4" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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225 <param name="col2" value="5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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226 <param name="selected_task" value="train" />
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227 <param name="selected_algorithm" value="SGDClassifier" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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228 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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229 <output name="outfile_fit" file="glm_model02" compare="sim_size" delta="5" />
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230 </test>
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231 <test>
34
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232 <param name="infile_model" value="glm_model02" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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233 <param name="infile_data" value="test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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234 <param name="selected_task" value="load" />
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235 <output name="outfile_predict" file="glm_result02" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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236 </test>
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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237 <test>
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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238 <param name="infile1" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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239 <param name="infile2" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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240 <param name="col1" value="1,2,3,4" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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241 <param name="col2" value="5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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242 <param name="selected_task" value="train" />
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243 <param name="selected_algorithm" value="RidgeClassifier" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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244 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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245 <output name="outfile_fit" file="glm_model03" compare="sim_size" delta="5" />
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246 </test>
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247 <test>
34
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248 <param name="infile_model" value="glm_model03" ftype="zip" />
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249 <param name="infile_data" value="test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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250 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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251 <output name="outfile_predict" file="glm_result03" />
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252 </test>
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253 <test>
34
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254 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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255 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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256 <param name="col1" value="1,2,3,4,5" />
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diff changeset
257 <param name="col2" value="6" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
258 <param name="selected_task" value="train" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
259 <param name="selected_algorithm" value="LinearRegression" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
260 <output name="outfile_fit" file="glm_model04" compare="sim_size" delta="5" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
261 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
262 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
263 <param name="infile_model" value="glm_model04" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
264 <param name="infile_data" value="regression_test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
265 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
266 <output name="outfile_predict" file="glm_result04" lines_diff="8" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
267 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
268 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
269 <param name="infile1" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
270 <param name="infile2" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
271 <param name="col1" value="1,2,3,4" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
272 <param name="col2" value="5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
273 <param name="selected_task" value="train" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
274 <param name="selected_algorithm" value="LogisticRegression" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
275 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
276 <output name="outfile_fit" file="glm_model05" compare="sim_size" delta="5" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
277 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
278 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
279 <param name="infile_model" value="glm_model05" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
280 <param name="infile_data" value="test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
281 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
282 <output name="outfile_predict" file="glm_result05" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
283 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
284 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
285 <param name="infile1" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
286 <param name="infile2" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
287 <param name="col1" value="1,2,3,4" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
288 <param name="col2" value="5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
289 <param name="selected_task" value="train" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
290 <param name="selected_algorithm" value="LogisticRegressionCV" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
291 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
292 <output name="outfile_fit" file="glm_model06" compare="sim_size" delta="5" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
293 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
294 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
295 <param name="infile_model" value="glm_model06" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
296 <param name="infile_data" value="test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
297 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
298 <output name="outfile_predict" file="glm_result06" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
299 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
300 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
301 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
302 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
303 <param name="col1" value="1,2,3,4,5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
304 <param name="col2" value="6" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
305 <param name="selected_task" value="train" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
306 <param name="selected_algorithm" value="Ridge" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
307 <param name="random_state" value="10" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
308 <output name="outfile_fit" file="glm_model07" compare="sim_size" delta="5" />
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
309 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
310 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
311 <param name="infile_model" value="glm_model07" ftype="zip" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
312 <param name="infile_data" value="regression_test.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
313 <param name="selected_task" value="load" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
314 <output name="outfile_predict">
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
315 <assert_contents>
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
316 <has_n_columns n="6" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
317 <has_text text="86.9702122735000" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
318 <has_text text="-1.0173960197" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
319 <has_text text="0.64184687433" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
320 <has_text text="-0.621522971207000" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
321 <has_text text="0.39001218449" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
322 <has_text text="0.596382816494397" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
323 <has_text text="-47.4101632272" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
324 <has_text text="-0.732777468453000" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
325 <has_text text="-1.0610977011" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
326 <has_text text="-1.099948005770000" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
327 <has_text text="0.58565796301" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
328 <has_text text="0.262144044202223" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
329 <has_text text="-206.99829512" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
330 <has_text text="0.7057412304" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
331 <has_text text="-1.332209237379999" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
332 </assert_contents>
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
333 </output>
0
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
334 </test>
6bc08bf6c6f3 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
335 <test>
34
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
336 <param name="infile1" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
337 <param name="infile2" value="train.tabular" ftype="tabular" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
338 <param name="col1" value="1,2,3,4" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
339 <param name="col2" value="5" />
b9a8876452cf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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340 <param name="selected_task" value="train" />
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341 <param name="selected_algorithm" value="Perceptron" />
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342 <param name="random_state" value="10" />
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343 <output name="outfile_fit" file="glm_model08" compare="sim_size" delta="5" />
0
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344 </test>
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345 <test>
34
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346 <param name="infile_model" value="glm_model08" ftype="zip" />
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347 <param name="infile_data" value="test.tabular" ftype="tabular" />
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348 <param name="selected_task" value="load" />
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349 <output name="outfile_predict" file="glm_result08" />
0
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350 </test>
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351 </tests>
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352 <help><![CDATA[
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353 ***What it does***
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354 This module implements a set of linear models for classification and regression such as: SGD classification and regression, Linear and Ridge regression and classification. This wrapper is using sklearn.linear_model module at its core. For information about linear models and their parameter settings please refer to `Scikit-learn generalized linear models`_.
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355
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356 .. _`Scikit-learn generalized linear models`: http://scikit-learn.org/stable/modules/linear_model.html
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357
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358 **1 - Methods**
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359 There are two groups of operations available:
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360
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361 1 - Train a model : A training set containing samples and their respective labels (or predicted values) are input. Based on the selected algorithm and options, an estimator object is fit to the data and is returned.
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362
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363 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset.
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364
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365 **2 - Trainig input**
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366 When you choose to train a model, you need a features dataset X and a labels set y. This tool expects tabular or sparse data for X and a single column for y (tabular). You can select a subset of columns in a tabular dataset as your features dataset or labels column. Below you find some examples:
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367
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368 **Sample tabular features dataset**
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369 The following training dataset contains 3 feature columns and a column containing class labels. You can simply select the first 3 columns as features and the last column as labels:
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370
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371 ::
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372
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373 4.01163365529 -6.10797684314 8.29829894763 1
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374 10.0788438916 1.59539821454 10.0684278289 0
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375 -5.17607775503 -0.878286135332 6.92941850665 2
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376 4.00975406235 -7.11847496542 9.3802423585 1
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377 4.61204065139 -5.71217537352 9.12509610964 1
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378
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379
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380 **Sample sparse features dataset**
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381 In this case you cannot specifiy a column range.
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382
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383 ::
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384
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385 4 1048577 8738
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386 1 271 0.020833
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387 1 1038 0.02461
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388 2 829017 0.016
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389 2 829437 0.012
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390 2 830752 0.025
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391 3 1047487 0.01
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392 3 1047980 0.02
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393 3 1048475 0.01
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394 4 608 0.016629
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395 4 1651 0.02519
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396 4 4053 0.04223
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397
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398
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399 **2 - Trainig output**
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400 The trained model is generated and output in the form of a binary file.
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401
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402
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403 **3 - Prediction input**
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404
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405 When you choose to load a model and do prediction, the tool expects an already trained estimator and a tabular dataset as input. The dataset contains new samples which you want to classify or predict regression values for.
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406
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407
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408 .. class:: warningmark
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409
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410 The number of feature columns must be the same in training and prediction datasets!
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411
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412
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413 **3 - Prediction output**
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414 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset.
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415
34
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416 ]]> </help>
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417 <expand macro="sklearn_citation" />
0
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418 </tool>