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annotate clf_metrics.xml @ 8:f361aac67330 draft

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author bgruening
date Sat, 28 Apr 2018 18:04:42 -0400
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children 3fb4723f5033
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@">
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2 <description>for classification 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 "$clf_metrics_script" '$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="clf_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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24 @COLUMNS_FUNCTION@
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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["clf_metrics"].get("header1", None) else None
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30 y_t = read_columns(
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31 "$clf_metrics.infile1",
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32 "$clf_metrics.col1",
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33 sep='\t',
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34 header=header,
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35 parse_dates=True
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36 )
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38 header='infer' if params["clf_metrics"].get("header2", None) else None
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39 y_p = read_columns(
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40 "$clf_metrics.infile2",
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41 "$clf_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
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47 options = params["clf_metrics"].get("options", {})
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48 print(options)
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49 if options and options.get('average', '') == 'None':
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50 options['average'] = None
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51 metric = params["clf_metrics"]["selected_metric"]
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52 metric_function = getattr(metrics, metric)
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53 res = metric_function(y_t,y_p,**options)
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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="clf_metrics">
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62 <param name="selected_metric" type="select" label="Metrics">
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63 <option value="accuracy_score" selected="true">Accuracy classification score</option>
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64 <option value="classification_report">Text report of the main classification metrics</option>
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65 <option value="f1_score">F1 score (aka balanced F-score or F-measure)</option>
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66 <option value="fbeta_score">F-beta score</option>
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67 <option value="hamming_loss">Average Hamming loss</option>
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68 <option value="jaccard_similarity_score">Jaccard similarity coefficient score</option>
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69 <option value="precision_recall_fscore_support">Compute precision, recall, F-measure and support for each class</option>
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70 <option value="precision_score">Precision</option>
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71 <option value="recall_score">Recall</option>
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72 <option value="zero_one_loss">Zero-one classification loss</option>
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73 <option value="auc">Area under the curve (AUC)</option>
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74 <option value="brier_score_loss">Brier score</option>
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75 <option value="matthews_corrcoef">Matthews correlation coefficient (MCC) for binary classes</option>
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76 <option value="confusion_matrix">Confusion matrix (evaluate the accuracy of a classification)</option>
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77 <option value="precision_recall_curve">Precision-recall pairs for different probability thresholds</option>
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78 <option value="roc_curve">Receiver operating characteristic (ROC)</option>
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79 <option value="hinge_loss">Average hinge loss (non-regularized)</option>
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80 <option value="log_loss">Log loss (aka logistic loss or cross-entropy loss)</option>
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81 <option value="average_precision_score">Average precision (AP) from prediction scores</option>
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82 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option>
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83 </param>
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84 <when value="accuracy_score">
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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-->
1
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88 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
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89 label="Normalize" help="If false, returns the number of correctly classified samples. Otherwise, returns the fraction of correctly classified samples. "/>
0
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90 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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91 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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92 <when value="classification_report">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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93 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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94 <section name="options" title="Advanced Options" expanded="False">
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95 <!--labels-->
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96 <!--target_names-->
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97 <!--sample_weight-->
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98 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help=""/>
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99 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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100 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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101 <when value="f1_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
102 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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103 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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104 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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105 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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106 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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107 <expand macro="average">
1
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108 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
0
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109 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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110 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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111 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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112 <when value="fbeta_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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113 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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114 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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115 <expand macro="beta"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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116 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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117 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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118 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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119 <expand macro="average">
1
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120 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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121 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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122 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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123 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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124 <when value="hamming_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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125 <expand macro="clf_inputs"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
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126 <!--section name="options" title="Advanced Options" expanded="False">
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diff changeset
127 <!- -classes- ->
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128 </section-->
0
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129 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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130 <when value="jaccard_similarity_score">
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131 <expand macro="clf_inputs"/>
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132 <section name="options" title="Advanced Options" expanded="False">
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133 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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134 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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135 </when>
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136 <when value="precision_recall_fscore_support">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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137 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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138 <section name="options" title="Advanced Options" expanded="False">
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139 <expand macro="beta"/>
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140 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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141 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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142 <!--warn_for-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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143 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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144 <expand macro="average">
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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145 <option value="binary" selected="true">Only report results for the class specified by pos_label. Applicable only on binary classification. (binary)</option>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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146 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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147 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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148 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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149 <when value="precision_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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150 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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151 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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152 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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153 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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154 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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155 <expand macro="average">
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
156 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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157 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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158 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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159 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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160 <when value="recall_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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161 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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162 <section name="options" title="Advanced Options" expanded="False">
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163 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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164 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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165 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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166 <expand macro="average">
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
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167 <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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168 </expand>
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169 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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170 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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171 <when value="zero_one_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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172 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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173 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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174 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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175 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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176 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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177 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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178 <when value="auc">
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179 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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180 <section name="options" title="Advanced Options" expanded="False">
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181 <param argument="reorder" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Assume an ascending curve in the case of ties" help="If the curve is non-ascending, the result will be wrong. "/>
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182 </section>
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183 </when>
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184 <when value="brier_score_loss">
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185 <expand macro="clf_inputs"/>
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186 <section name="options" title="Advanced Options" expanded="False">
1
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187 <!--weights-->
0
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188 <expand macro="pos_label"/>
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189 </section>
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190 </when>
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191 <when value="matthews_corrcoef">
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192 <expand macro="clf_inputs"/>
1
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193 <!--section name="options" title="Advanced Options" expanded="False">
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194 </section-->
0
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195 </when>
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196 <when value="confusion_matrix">
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197 <expand macro="clf_inputs"/>
1
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198 <!--section name="options" title="Advanced Options" expanded="False">
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199 <!- -labels- ->
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200 </section-->
0
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201 </when>
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202 <when value="precision_recall_curve">
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203 <expand macro="clf_inputs"/>
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204 <section name="options" title="Advanced Options" expanded="False">
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205 <expand macro="pos_label"/>
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206 <!--sample_weight-->
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207 </section>
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208 </when>
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209 <when value="roc_curve">
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210 <expand macro="clf_inputs"/>
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211 <section name="options" title="Advanced Options" expanded="False">
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212 <!--sample_weight-->
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213 <expand macro="pos_label"/>
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214 <param argument="drop_intermediate" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label=" Drop suboptimal thresholds" help="This is useful in order to create lighter ROC curves. "/>
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215 </section>
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216 </when>
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217 <when value="hinge_loss">
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218 <expand macro="clf_inputs" multiple="true"/>
1
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219 <!--section name="options" title="Advanced Options" expanded="False">
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220 <!- -labels- ->
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221 <!- -sample_weight- ->
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222 </section-->
0
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223 </when>
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224 <when value="log_loss">
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225 <expand macro="clf_inputs" multiple="true"/>
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226 <section name="options" title="Advanced Options" expanded="False">
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227 <!--sample_weight-->
1
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228 <param argument="eps" type="float" value="1e-15" label="Clipping factor"
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229 help="Log loss is undefined for p=0 or p=1, so probabilities are clipped to max(eps, min(1 - eps, p)). "/>
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230 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
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231 label="Normalize" help="If true, returns the mean loss per sample. Otherwise, returns the sum of the per-sample losses. "/>
0
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232 </section>
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233 </when>
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234 <when value="average_precision_score">
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235 <expand macro="clf_inputs" multiple1="true" multiple="true"/>
1
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236 <!-- section name="options" title="Advanced Options" expanded="False">
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237 <!- -average='macro', sample_weight=None- ->
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238 </section-->
0
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239 </when>
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240 <when value="roc_auc_score">
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241 <expand macro="clf_inputs" multiple1="true" multiple="true"/>
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242 <section name="options" title="Advanced Options" expanded="False">
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243 <expand macro="average">
1
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244 <option value="macro" selected="true">Calculate metrics for each label, and find their unweighted mean. (macro)</option>
0
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245 </expand>
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246 </section>
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247 </when>
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248 </conditional>
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249 </inputs>
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250 <outputs>
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251 <data format="txt" name="outfile"/>
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252 </outputs>
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253 <tests>
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254 <test>
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255 <param name="selected_metric" value="accuracy_score"/>
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256 <param name="infile1" value="y.tabular" ftype="tabular"/>
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257 <param name="col1" value="1"/>
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258 <param name="infile2" value="y.tabular" ftype="tabular"/>
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259 <param name="col2" value="2"/>
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260 <output name="outfile" file="accuracy_score.txt"/>
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261 </test>
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262 <test>
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263 <param name="selected_metric" value="classification_report"/>
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264 <param name="infile1" value="y.tabular" ftype="tabular"/>
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265 <param name="col1" value="1"/>
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266 <param name="infile2" value="y.tabular" ftype="tabular"/>
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267 <param name="col2" value="2"/>
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268 <output name="outfile" file="classification_report.txt"/>
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269 </test>
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270 <test>
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271 <param name="selected_metric" value="f1_score"/>
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272 <param name="infile1" value="y.tabular" ftype="tabular"/>
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273 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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274 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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275 <param name="col2" value="2"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
diff changeset
276 <param name="average" value="micro"/>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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277 <output name="outfile" file="f1_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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278 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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279 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
280 <param name="selected_metric" value="fbeta_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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281 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
282 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
283 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
284 <param name="col2" value="2"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
diff changeset
285 <param name="average" value="micro"/>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
286 <output name="outfile" file="fbeta_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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287 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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288 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
289 <param name="selected_metric" value="hamming_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
290 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
291 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
292 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
293 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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294 <output name="outfile" file="hamming_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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295 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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296 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
297 <param name="selected_metric" value="jaccard_similarity_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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298 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
299 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
300 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
301 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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302 <output name="outfile" file="jaccard_similarity_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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303 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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304 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
305 <param name="selected_metric" value="precision_recall_fscore_support"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
306 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
307 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
308 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
309 <param name="col2" value="2"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
diff changeset
310 <param name="average" value="micro"/>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
311 <output name="outfile" file="precision_recall_fscore_support.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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312 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
313 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
314 <param name="selected_metric" value="precision_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
315 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
316 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
317 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
318 <param name="col2" value="2"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 0
diff changeset
319 <param name="average" value="micro"/>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
320 <output name="outfile" file="precision_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
321 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
322 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
323 <param name="selected_metric" value="recall_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
324 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
325 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
326 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
327 <param name="col2" value="2"/>
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 0
diff changeset
328 <param name="average" value="micro"/>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
329 <output name="outfile" file="recall_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
330 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
331 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
332 <param name="selected_metric" value="zero_one_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
333 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
334 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
335 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
336 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
337 <output name="outfile" file="zero_one_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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338 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
339 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
340 <param name="selected_metric" value="auc"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
341 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
342 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
343 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
344 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
345 <param name="reorder" value="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
346 <output name="outfile" file="auc.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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347 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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348 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
349 <param name="selected_metric" value="brier_score_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
350 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
351 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
352 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
353 <param name="col2" value="3"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
354 <output name="outfile" file="brier_score_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
355 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
356 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
357 <param name="selected_metric" value="matthews_corrcoef"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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parents:
diff changeset
358 <param name="infile1" value="y.tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
359 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
360 <param name="infile2" value="y.tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
361 <param name="col2" value="7"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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362 <output name="outfile" file="matthews_corrcoef.txt"/>
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363 </test>
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364 <test>
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365 <param name="selected_metric" value="confusion_matrix"/>
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366 <param name="infile1" value="y.tabular" ftype="tabular"/>
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367 <param name="col1" value="1"/>
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368 <param name="infile2" value="y.tabular" ftype="tabular"/>
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369 <param name="col2" value="2"/>
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370 <output name="outfile" file="confusion_matrix.txt"/>
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371 </test>
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372 <test>
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373 <param name="selected_metric" value="precision_recall_curve"/>
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374 <param name="infile1" value="y.tabular" ftype="tabular"/>
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375 <param name="col1" value="6"/>
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376 <param name="infile2" value="y.tabular" ftype="tabular"/>
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377 <param name="col2" value="7"/>
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378 <output name="outfile" file="precision_recall_curve.txt"/>
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379 </test>
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380 <test>
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381 <param name="selected_metric" value="roc_curve"/>
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382 <param name="infile1" value="y.tabular" ftype="tabular"/>
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383 <param name="col1" value="6"/>
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384 <param name="infile2" value="y.tabular" ftype="tabular"/>
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385 <param name="col2" value="7"/>
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386 <output name="outfile" file="roc_curve.txt"/>
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387 </test>
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388 <test>
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389 <param name="selected_metric" value="hinge_loss"/>
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390 <param name="infile1" value="y.tabular" ftype="tabular"/>
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391 <param name="col1" value="1"/>
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392 <param name="infile2" value="y.tabular" ftype="tabular"/>
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393 <param name="col2" value="8,9,10"/>
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394 <output name="outfile" file="hinge_loss.txt"/>
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395 </test>
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396 <test>
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397 <param name="selected_metric" value="log_loss"/>
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398 <param name="infile1" value="y.tabular" ftype="tabular"/>
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399 <param name="col1" value="2"/>
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400 <param name="infile2" value="y.tabular" ftype="tabular"/>
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401 <param name="col2" value="3,4,5"/>
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402 <output name="outfile" file="log_loss.txt"/>
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403 </test>
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404 <test>
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405 <param name="selected_metric" value="average_precision_score"/>
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406 <param name="infile1" value="y.tabular" ftype="tabular"/>
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407 <param name="col1" value="6"/>
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408 <param name="infile2" value="y.tabular" ftype="tabular"/>
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409 <param name="col2" value="7"/>
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410 <output name="outfile" file="average_precision_score.txt"/>
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411 </test>
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412 <test>
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413 <param name="selected_metric" value="roc_auc_score"/>
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414 <param name="infile1" value="y.tabular" ftype="tabular"/>
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415 <param name="col1" value="6"/>
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416 <param name="infile2" value="y.tabular" ftype="tabular"/>
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417 <param name="col2" value="7"/>
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418 <output name="outfile" file="roc_auc_score.txt"/>
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419 </test>
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420 </tests>
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421 <help>
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422 <![CDATA[
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423 **What it does**
1
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424 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
0
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425 sklearn.metrics package.
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426 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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427
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428 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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429 ]]>
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430 </help>
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431 <expand macro="sklearn_citation"/>
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432 </tool>