Mercurial > repos > bgruening > sklearn_regression_metrics

annotate regression_metrics.xml @ 17:25b74e5f42f4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author bgruening
date Tue, 14 May 2019 17:53:59 -0400
parents d2d36ee2c061
children 3cc8a461bc5d
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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"/>
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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
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 sys.path.insert(0, '$__tool_directory__')
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25 from utils import read_columns
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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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30
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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31 header='infer' if params["regression_metrics"]["header1"] else None
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32 column_option = params["regression_metrics"]["column_selector_options_1"]["selected_column_selector_option"]
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3ce5d492b568 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
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33 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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34 c = params["regression_metrics"]["column_selector_options_1"]["col1"]
c5feb1a67e9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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35 else:
c5feb1a67e9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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36 c = None
0
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37 y_t = read_columns(
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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38 "$regression_metrics.infile1",
3
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39 c = c,
c5feb1a67e9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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40 c_option = column_option,
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41 sep='\t',
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42 header=header,
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43 parse_dates=True)
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44
ca05b5889dfc 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(
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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52 "$regression_metrics.infile2",
3
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53 c = c,
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54 c_option = column_option,
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55 sep='\t',
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56 header=header,
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57 parse_dates=True)
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58
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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59 options = params["regression_metrics"].get("options", {})
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60 if options and options.get('average', '') == 'None':
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61 options['average'] = None
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62 metric = params["regression_metrics"]["selected_metric"]
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63 metric_function = getattr(metrics, metric)
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64 res = metric_function(y_t,y_p,**options)
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65 res= format(res, '.4f')
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66 with open("$outfile", 'w+') as out_file:
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67 out_file.write( metric + ' : ' + '\n' + str(res) + '\n' )
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68
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69 ]]>
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70 </configfile>
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71 </configfiles>
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72 <inputs>
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73 <conditional name="regression_metrics">
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74 <param name="selected_metric" type="select" label="Metrics">
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75 <option value="explained_variance_score" selected="true">explained_variance_score - Explained variance regression score function</option>
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76 <option value="mean_absolute_error">mean_absolute_error - Mean absolute error regression loss</option>
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77 <option value="mean_squared_error">mean_squared_error - Mean squared error regression loss</option>
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78 <option value="mean_squared_log_error">mean_squared_log_error - Mean squared logarithmic error regression loss</option>
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79 <option value="median_absolute_error">median_absolute_error - Median absolute error regression loss</option>
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80 <option value="r2_score">r2_score - R^2 (coefficient of determination) regression score function</option>
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81 </param>
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82 <when value="explained_variance_score">
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83 <expand macro="clf_inputs"/>
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84 <!--section name="options" title="Advanced Options" expanded="False">
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85 <!- -sample_weight- ->
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diff changeset
86 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
87 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
88 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
89 <when value="mean_absolute_error">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
90 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
91 <!--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
92 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
93 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
94 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
95 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
96 <when value="mean_squared_error">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
97 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
98 <!--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
99 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
100 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
101 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
102 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
103 <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
104 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
105 <!--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
106 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
107 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
108 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
109 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
110 <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
111 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
112 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
113 <when value="r2_score">
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
114 <expand macro="clf_inputs"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
115 <!--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
116 <!- -sample_weight- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
117 <!- -multioutput- ->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
118 </section-->
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
119 </when>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
120 </conditional>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
121 </inputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
122 <outputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
123 <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
124 </outputs>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
125 <tests>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
126 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
127 <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
128 <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
129 <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
130 <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
131 <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
132 <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
133 <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
134 <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
135 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
136 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
146 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
147 <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
148 <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
149 <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
150 <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
151 <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
152 <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
153 <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
154 <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
155 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
156 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
157 <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
158 <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
159 <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
160 <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
161 <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
162 <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
163 <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
164 <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
165 </test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
166 <test>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
167 <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
168 <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
169 <param name="header1" value="True"/>
4
ef365d71514e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 64158f357e708f0b60d2669d92d614f7aee34c0e
bgruening
parents: 3
diff changeset
170 <param name="selected_column_selector_option" value="all_but_by_index_number"/>
ef365d71514e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 64158f357e708f0b60d2669d92d614f7aee34c0e
bgruening
parents: 3
diff changeset
171 <param name="col1" value="2"/>
0
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
172 <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
173 <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
174 <param name="col2" value="2"/>
ca05b5889dfc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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175 <output name="outfile" file="regression_metrics_result05"/>
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176 </test>
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177 <test>
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178 <param name="selected_metric" value="r2_score"/>
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179 <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/>
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180 <param name="header1" value="True"/>
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181 <param name="col1" value="1"/>
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182 <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/>
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183 <param name="header2" value="True"/>
4
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184 <param name="selected_column_selector_option2" value="all_but_by_index_number"/>
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185 <param name="col2" value="1"/>
0
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186 <output name="outfile" file="regression_metrics_result06"/>
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187 </test>
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188 </tests>
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189 <help>
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190 <![CDATA[
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191 **What it does**
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192 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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193 sklearn.metrics package.
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194 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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195
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196 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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197 ]]>
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198 </help>
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199 <expand macro="sklearn_citation"/>
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200 </tool>