Mercurial > repos > bgruening > sklearn_regression_metrics

annotate regression_metrics.xml @ 0:ca05b5889dfc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
author bgruening
date Sat, 28 Apr 2018 18:05:04 -0400
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children c5feb1a67e9b
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ca05b5889dfc 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"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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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 ]]>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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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
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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20 import pandas
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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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 @COLUMNS_FUNCTION@
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25
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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26 input_json_path = sys.argv[1]
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27 params = json.load(open(input_json_path, "r"))
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28
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29 header='infer' if params["regression_metrics"]["header1"] else None
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30 y_t = read_columns(
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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31 "$regression_metrics.infile1",
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32 "$regression_metrics.col1",
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33 sep='\t',
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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34 header=header,
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35 parse_dates=True
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36 )
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37
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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38 header='infer' if params["regression_metrics"]["header2"] else None
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39 y_p = read_columns(
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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40 "$regression_metrics.infile2",
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41 "$regression_metrics.col2",
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42 sep='\t',
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43 header=header,
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44 parse_dates=True
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45 )
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46
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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47 options = params["regression_metrics"].get("options", {})
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48 if options and options.get('average', '') == 'None':
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49 options['average'] = None
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50 metric = params["regression_metrics"]["selected_metric"]
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51 metric_function = getattr(metrics, metric)
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52 res = metric_function(y_t,y_p,**options)
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53 res= format(res, '.4f')
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54 with open("$outfile", 'w+') as out_file:
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55 out_file.write( metric + ' : ' + '\n' + str(res) + '\n' )
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56
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57 ]]>
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58 </configfile>
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59 </configfiles>
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60 <inputs>
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61 <conditional name="regression_metrics">
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62 <param name="selected_metric" type="select" label="Metrics">
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63 <option value="explained_variance_score" selected="true">explained_variance_score - Explained variance regression score function</option>
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64 <option value="mean_absolute_error">mean_absolute_error - Mean absolute error regression loss</option>
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65 <option value="mean_squared_error">mean_squared_error - Mean squared error regression loss</option>
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66 <option value="mean_squared_log_error">mean_squared_log_error - Mean squared logarithmic error regression loss</option>
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67 <option value="median_absolute_error">median_absolute_error - Median absolute error regression loss</option>
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68 <option value="r2_score">r2_score - R^2 (coefficient of determination) regression score function</option>
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69 </param>
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70 <when value="explained_variance_score">
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71 <expand macro="clf_inputs"/>
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72 <!--section name="options" title="Advanced Options" expanded="False">
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73 <!- -sample_weight- ->
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74 <!- -multioutput- ->
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75 </section-->
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76 </when>
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77 <when value="mean_absolute_error">
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78 <expand macro="clf_inputs"/>
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79 <!--section name="options" title="Advanced Options" expanded="False">
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80 <!- -sample_weight- ->
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81 <!- -multioutput- ->
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82 </section-->
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83 </when>
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84 <when value="mean_squared_error">
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85 <expand macro="clf_inputs"/>
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86 <!--section name="options" title="Advanced Options" expanded="False">
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87 <!- -sample_weight- ->
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88 <!- -multioutput- ->
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diff changeset
89 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
90 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
91 <when value="mean_squared_log_error">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
92 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
93 <!--section name="options" title="Advanced Options" expanded="False">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
94 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
95 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
96 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
97 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
98 <when value="median_absolute_error">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
99 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
100 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
101 <when value="r2_score">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
102 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
103 <!--section name="options" title="Advanced Options" expanded="False">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
104 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
105 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
106 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
107 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
108 </conditional>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
109 </inputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
110 <outputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
111 <data format="txt" name="outfile"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
112 </outputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
113 <tests>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
114 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
115 <param name="selected_metric" value="explained_variance_score"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
116 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
117 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
118 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
119 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
120 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
121 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
122 <output name="outfile" file="regression_metrics_result01"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
123 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
124 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
125 <param name="selected_metric" value="mean_absolute_error"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
126 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
127 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
128 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
129 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
130 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
131 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
132 <output name="outfile" file="regression_metrics_result02"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
133 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
134 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
135 <param name="selected_metric" value="mean_squared_error"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
136 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
137 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
138 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
139 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
140 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
141 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
142 <output name="outfile" file="regression_metrics_result03"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
143 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
144 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
145 <param name="selected_metric" value="mean_squared_log_error"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
146 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
147 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
148 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
149 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
150 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
151 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
152 <output name="outfile" file="regression_metrics_result04"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
153 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
154 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
155 <param name="selected_metric" value="median_absolute_error"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
156 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
157 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
158 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
159 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
160 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
161 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
162 <output name="outfile" file="regression_metrics_result05"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
163 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
164 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
165 <param name="selected_metric" value="r2_score"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
166 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
167 <param name="header1" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
168 <param name="col1" value="1"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
169 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
170 <param name="header2" value="True"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
171 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
172 <output name="outfile" file="regression_metrics_result06"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
173 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
174 </tests>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
175 <help>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
176 <![CDATA[
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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177 **What it does**
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178 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
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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179 sklearn.metrics package.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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180 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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181
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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182 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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183 ]]>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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184 </help>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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185 <expand macro="sklearn_citation"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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186 </tool>