annotate regression_metrics.xml @ 16:268ecaf96b68 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
author bgruening
date Sun, 30 Dec 2018 01:59:44 -0500
parents 625beb4e5000
children 40ee30b5e456
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e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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1 <tool id="sklearn_regression_metrics" name="Calculate metrics" version="@VERSION@">
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2 <description>for regression performance</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$regression_metrics_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="regression_metrics_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import numpy as np
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22 from sklearn import metrics
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23
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24 exec(open("$__tool_directory__/utils.py").read(), globals())
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25
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26 input_json_path = sys.argv[1]
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27 with open(input_json_path, "r") as param_handler:
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28 params = json.load(param_handler)
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29
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30 header='infer' if params["regression_metrics"]["header1"] else None
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31 column_option = params["regression_metrics"]["column_selector_options_1"]["selected_column_selector_option"]
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32 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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33 c = params["regression_metrics"]["column_selector_options_1"]["col1"]
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34 else:
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35 c = None
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36 y_t = read_columns(
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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37 "$regression_metrics.infile1",
3
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38 c = c,
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39 c_option = column_option,
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40 sep='\t',
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41 header=header,
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42 parse_dates=True
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43 )
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44
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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45 header='infer' if params["regression_metrics"]["header2"] else None
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46 column_option = params["regression_metrics"]["column_selector_options_2"]["selected_column_selector_option2"]
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47 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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48 c = params["regression_metrics"]["column_selector_options_2"]["col2"]
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49 else:
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50 c = None
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51 y_p = read_columns(
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52 "$regression_metrics.infile2",
3
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53 c = c,
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54 c_option = column_option,
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55 sep='\t',
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56 header=header,
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57 parse_dates=True
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58 )
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59
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60 options = params["regression_metrics"].get("options", {})
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61 if options and options.get('average', '') == 'None':
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62 options['average'] = None
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63 metric = params["regression_metrics"]["selected_metric"]
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64 metric_function = getattr(metrics, metric)
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65 res = metric_function(y_t,y_p,**options)
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66 res= format(res, '.4f')
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67 with open("$outfile", 'w+') as out_file:
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68 out_file.write( metric + ' : ' + '\n' + str(res) + '\n' )
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69
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70 ]]>
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71 </configfile>
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72 </configfiles>
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73 <inputs>
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74 <conditional name="regression_metrics">
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75 <param name="selected_metric" type="select" label="Metrics">
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76 <option value="explained_variance_score" selected="true">explained_variance_score - Explained variance regression score function</option>
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77 <option value="mean_absolute_error">mean_absolute_error - Mean absolute error regression loss</option>
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78 <option value="mean_squared_error">mean_squared_error - Mean squared error regression loss</option>
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79 <option value="mean_squared_log_error">mean_squared_log_error - Mean squared logarithmic error regression loss</option>
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80 <option value="median_absolute_error">median_absolute_error - Median absolute error regression loss</option>
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81 <option value="r2_score">r2_score - R^2 (coefficient of determination) regression score function</option>
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82 </param>
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83 <when value="explained_variance_score">
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84 <expand macro="clf_inputs"/>
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85 <!--section name="options" title="Advanced Options" expanded="False">
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86 <!- -sample_weight- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
87 <!- -multioutput- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
88 </section-->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
89 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
90 <when value="mean_absolute_error">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
91 <expand macro="clf_inputs"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
92 <!--section name="options" title="Advanced Options" expanded="False">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
93 <!- -sample_weight- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
94 <!- -multioutput- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
95 </section-->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
96 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
97 <when value="mean_squared_error">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
98 <expand macro="clf_inputs"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
99 <!--section name="options" title="Advanced Options" expanded="False">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
100 <!- -sample_weight- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
101 <!- -multioutput- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
102 </section-->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
103 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
104 <when value="mean_squared_log_error">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
105 <expand macro="clf_inputs"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
106 <!--section name="options" title="Advanced Options" expanded="False">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
107 <!- -sample_weight- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
108 <!- -multioutput- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
109 </section-->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
110 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
111 <when value="median_absolute_error">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
112 <expand macro="clf_inputs"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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diff changeset
113 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
114 <when value="r2_score">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
115 <expand macro="clf_inputs"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
116 <!--section name="options" title="Advanced Options" expanded="False">
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
117 <!- -sample_weight- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
118 <!- -multioutput- ->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
119 </section-->
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
120 </when>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
121 </conditional>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
122 </inputs>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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diff changeset
123 <outputs>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
124 <data format="txt" name="outfile"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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diff changeset
125 </outputs>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
126 <tests>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
127 <test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
128 <param name="selected_metric" value="explained_variance_score"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
129 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
130 <param name="header1" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
131 <param name="col1" value="1"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
132 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
133 <param name="header2" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
134 <param name="col2" value="2"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
135 <output name="outfile" file="regression_metrics_result01"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
136 </test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
137 <test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
138 <param name="selected_metric" value="mean_absolute_error"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
139 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
140 <param name="header1" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
141 <param name="col1" value="1"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
142 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
143 <param name="header2" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
144 <param name="col2" value="2"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
145 <output name="outfile" file="regression_metrics_result02"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
146 </test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
147 <test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
148 <param name="selected_metric" value="mean_squared_error"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
149 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
150 <param name="header1" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
151 <param name="col1" value="1"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
152 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
153 <param name="header2" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
154 <param name="col2" value="2"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
155 <output name="outfile" file="regression_metrics_result03"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
156 </test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
157 <test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
158 <param name="selected_metric" value="mean_squared_log_error"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
159 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
160 <param name="header1" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
161 <param name="col1" value="1"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
162 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
163 <param name="header2" value="True"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
164 <param name="col2" value="2"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
165 <output name="outfile" file="regression_metrics_result04"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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diff changeset
166 </test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
167 <test>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
168 <param name="selected_metric" value="median_absolute_error"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
169 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
170 <param name="header1" value="True"/>
4
64c87ceb6766 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 64158f357e708f0b60d2669d92d614f7aee34c0e
bgruening
parents: 3
diff changeset
171 <param name="selected_column_selector_option" value="all_but_by_index_number"/>
64c87ceb6766 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 64158f357e708f0b60d2669d92d614f7aee34c0e
bgruening
parents: 3
diff changeset
172 <param name="col1" value="2"/>
0
e1a494495d9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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173 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
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174 <param name="header2" value="True"/>
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175 <param name="col2" value="2"/>
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176 <output name="outfile" file="regression_metrics_result05"/>
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177 </test>
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178 <test>
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179 <param name="selected_metric" value="r2_score"/>
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180 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
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181 <param name="header1" value="True"/>
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182 <param name="col1" value="1"/>
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183 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
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184 <param name="header2" value="True"/>
4
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185 <param name="selected_column_selector_option2" value="all_but_by_index_number"/>
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186 <param name="col2" value="1"/>
0
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187 <output name="outfile" file="regression_metrics_result06"/>
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188 </test>
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189 </tests>
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190 <help>
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191 <![CDATA[
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192 **What it does**
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193 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on
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194 sklearn.metrics package.
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195 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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196
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197 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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198 ]]>
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199 </help>
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200 <expand macro="sklearn_citation"/>
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201 </tool>