Mercurial > repos > bgruening > sklearn_regression_metrics
view regression_metrics.xml @ 23:649017be1c60 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
author | bgruening |
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date | Thu, 07 Nov 2019 05:32:45 -0500 |
parents | 28d51b976c29 |
children | 0cc5098a9bff |
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<tool id="sklearn_regression_metrics" name="Calculate metrics" version="@VERSION@"> <description>for regression performance</description> <macros> <import>main_macros.xml</import> </macros> <expand macro="python_requirements"/> <expand macro="macro_stdio"/> <version_command>echo "@VERSION@"</version_command> <command> <![CDATA[ python "$regression_metrics_script" '$inputs' ]]> </command> <configfiles> <inputs name="inputs" /> <configfile name="regression_metrics_script"> <![CDATA[ import sys import json import pandas import numpy as np from sklearn import metrics from galaxy_ml.utils import read_columns input_json_path = sys.argv[1] with open(input_json_path, "r") as param_handler: params = json.load(param_handler) header='infer' if params["regression_metrics"]["header1"] else None column_option = params["regression_metrics"]["column_selector_options_1"]["selected_column_selector_option"] if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: c = params["regression_metrics"]["column_selector_options_1"]["col1"] else: c = None y_t = read_columns( "$regression_metrics.infile1", c = c, c_option = column_option, sep='\t', header=header, parse_dates=True) header='infer' if params["regression_metrics"]["header2"] else None column_option = params["regression_metrics"]["column_selector_options_2"]["selected_column_selector_option2"] if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: c = params["regression_metrics"]["column_selector_options_2"]["col2"] else: c = None y_p = read_columns( "$regression_metrics.infile2", c = c, c_option = column_option, sep='\t', header=header, parse_dates=True) options = params["regression_metrics"].get("options", {}) if options and options.get('average', '') == 'None': options['average'] = None metric = params["regression_metrics"]["selected_metric"] metric_function = getattr(metrics, metric) res = metric_function(y_t,y_p,**options) res= format(res, '.4f') with open("$outfile", 'w+') as out_file: out_file.write( metric + ' : ' + '\n' + str(res) + '\n' ) ]]> </configfile> </configfiles> <inputs> <conditional name="regression_metrics"> <param name="selected_metric" type="select" label="Metrics"> <option value="explained_variance_score" selected="true">explained_variance_score - Explained variance regression score function</option> <option value="mean_absolute_error">mean_absolute_error - Mean absolute error regression loss</option> <option value="mean_squared_error">mean_squared_error - Mean squared error regression loss</option> <option value="mean_squared_log_error">mean_squared_log_error - Mean squared logarithmic error regression loss</option> <option value="median_absolute_error">median_absolute_error - Median absolute error regression loss</option> <option value="r2_score">r2_score - R^2 (coefficient of determination) regression score function</option> </param> <when value="explained_variance_score"> <expand macro="clf_inputs"/> <!--section name="options" title="Advanced Options" expanded="False"> <!- -sample_weight- -> <!- -multioutput- -> </section--> </when> <when value="mean_absolute_error"> <expand macro="clf_inputs"/> <!--section name="options" title="Advanced Options" expanded="False"> <!- -sample_weight- -> <!- -multioutput- -> </section--> </when> <when value="mean_squared_error"> <expand macro="clf_inputs"/> <!--section name="options" title="Advanced Options" expanded="False"> <!- -sample_weight- -> <!- -multioutput- -> </section--> </when> <when value="mean_squared_log_error"> <expand macro="clf_inputs"/> <!--section name="options" title="Advanced Options" expanded="False"> <!- -sample_weight- -> <!- -multioutput- -> </section--> </when> <when value="median_absolute_error"> <expand macro="clf_inputs"/> </when> <when value="r2_score"> <expand macro="clf_inputs"/> <!--section name="options" title="Advanced Options" expanded="False"> <!- -sample_weight- -> <!- -multioutput- -> </section--> </when> </conditional> </inputs> <outputs> <data format="txt" name="outfile"/> </outputs> <tests> <test> <param name="selected_metric" value="explained_variance_score"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="col1" value="1"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="col2" value="2"/> <output name="outfile" file="regression_metrics_result01"/> </test> <test> <param name="selected_metric" value="mean_absolute_error"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="col1" value="1"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="col2" value="2"/> <output name="outfile" file="regression_metrics_result02"/> </test> <test> <param name="selected_metric" value="mean_squared_error"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="col1" value="1"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="col2" value="2"/> <output name="outfile" file="regression_metrics_result03"/> </test> <test> <param name="selected_metric" value="mean_squared_log_error"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="col1" value="1"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="col2" value="2"/> <output name="outfile" file="regression_metrics_result04"/> </test> <test> <param name="selected_metric" value="median_absolute_error"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="selected_column_selector_option" value="all_but_by_index_number"/> <param name="col1" value="2"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="col2" value="2"/> <output name="outfile" file="regression_metrics_result05"/> </test> <test> <param name="selected_metric" value="r2_score"/> <param name="infile1" value="regression_test_y.tabular" ftype="tabular"/> <param name="header1" value="True"/> <param name="col1" value="1"/> <param name="infile2" value="regression_test_y.tabular" ftype="tabular"/> <param name="header2" value="True"/> <param name="selected_column_selector_option2" value="all_but_by_index_number"/> <param name="col2" value="1"/> <output name="outfile" file="regression_metrics_result06"/> </test> </tests> <help> <![CDATA[ **What it does** 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 sklearn.metrics package. For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_. .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics ]]> </help> <expand macro="sklearn_citation"/> </tool>