Mercurial > repos > bgruening > sklearn_clf_metrics

annotate clf_metrics.xml @ 35:3c5034b0d775 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 21:08:12 +0000
parents e801d2034575
children 0a12776d3e8d
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3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@" profile="20.05">
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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>
35
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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 import sys
0
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23 from sklearn import metrics
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24 from galaxy_ml.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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31 header='infer' if params["clf_metrics"].get("header1", None) else None
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32 column_option = params["clf_metrics"]["column_selector_options_1"]["selected_column_selector_option"]
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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["clf_metrics"]["column_selector_options_1"]["col1"]
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35 else:
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36 c = None
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37 y_t = read_columns(
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38 "$clf_metrics.infile1",
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39 c = c,
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40 c_option = column_option,
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41 sep='\t',
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42 header=header,
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43 parse_dates=True)
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45 header='infer' if params["clf_metrics"].get("header2", None) else None
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46 column_option = params["clf_metrics"]["column_selector_options_2"]["selected_column_selector_option2"]
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47 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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48 c = params["clf_metrics"]["column_selector_options_2"]["col2"]
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49 else:
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50 c = None
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51 y_p = read_columns(
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52 "$clf_metrics.infile2",
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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
1
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59 options = params["clf_metrics"].get("options", {})
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60 print(options)
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61 if options and options.get('average', '') == 'None':
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62 options['average'] = None
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63 metric = params["clf_metrics"]["selected_metric"]
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64 metric_function = getattr(metrics, metric)
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65 res = metric_function(y_t,y_p,**options)
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66 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="clf_metrics">
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74 <param name="selected_metric" type="select" label="Metrics">
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75 <option value="accuracy_score" selected="true">Accuracy classification score</option>
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76 <option value="classification_report">Text report of the main classification metrics</option>
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77 <option value="f1_score">F1 score (aka balanced F-score or F-measure)</option>
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78 <option value="fbeta_score">F-beta score</option>
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79 <option value="hamming_loss">Average Hamming loss</option>
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80 <option value="jaccard_similarity_score">Jaccard similarity coefficient score</option>
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81 <option value="precision_recall_fscore_support">Compute precision, recall, F-measure and support for each class</option>
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82 <option value="precision_score">Precision</option>
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83 <option value="recall_score">Recall</option>
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84 <option value="zero_one_loss">Zero-one classification loss</option>
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85 <option value="auc">Area under the curve (AUC)</option>
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86 <option value="brier_score_loss">Brier score</option>
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87 <option value="matthews_corrcoef">Matthews correlation coefficient (MCC) for binary classes</option>
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88 <option value="confusion_matrix">Confusion matrix (evaluate the accuracy of a classification)</option>
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89 <option value="precision_recall_curve">Precision-recall pairs for different probability thresholds</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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90 <option value="roc_curve">Receiver operating characteristic (ROC)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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91 <option value="hinge_loss">Average hinge loss (non-regularized)</option>
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92 <option value="log_loss">Log loss (aka logistic loss or cross-entropy loss)</option>
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93 <option value="average_precision_score">Average precision (AP) from prediction scores</option>
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94 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option>
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95 </param>
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96 <when value="accuracy_score">
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97 <expand macro="clf_inputs" />
0
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98 <section name="options" title="Advanced Options" expanded="False">
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99 <!--sample_weight-->
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100 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" 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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101 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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102 </when>
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103 <when value="classification_report">
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104 <expand macro="clf_inputs" />
0
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105 <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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106 <!--labels-->
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107 <!--target_names-->
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108 <!--sample_weight-->
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109 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help="" />
0
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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="f1_score">
35
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113 <expand macro="clf_inputs" />
0
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114 <section name="options" title="Advanced Options" expanded="False">
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115 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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116 <!--sample_weight-->
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117 <expand macro="pos_label" default_value="1" />
0
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118 <expand macro="average">
1
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119 <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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120 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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121 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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122 </when>
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123 <when value="fbeta_score">
35
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124 <expand macro="clf_inputs" />
0
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125 <section name="options" title="Advanced Options" expanded="False">
35
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diff changeset
126 <expand macro="beta" />
0
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127 <!--labels-->
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128 <!--sample_weight-->
35
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129 <expand macro="pos_label" default_value="1" />
0
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130 <expand macro="average">
1
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131 <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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132 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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133 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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134 </when>
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135 <when value="hamming_loss">
35
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136 <expand macro="clf_inputs" />
1
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137 <!--section name="options" title="Advanced Options" expanded="False">
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138 <!- -classes- ->
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139 </section-->
0
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140 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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141 <when value="jaccard_similarity_score">
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142 <expand macro="clf_inputs" />
0
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143 <section name="options" title="Advanced Options" expanded="False">
35
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144 <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. " />
0
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145 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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146 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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147 <when value="precision_recall_fscore_support">
35
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148 <expand macro="clf_inputs" />
0
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149 <section name="options" title="Advanced Options" expanded="False">
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
150 <expand macro="beta" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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151 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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152 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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153 <!--warn_for-->
35
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154 <expand macro="pos_label" default_value="1" />
0
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155 <expand macro="average">
1
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156 <option value="binary" selected="true">Only report results for the class specified by pos_label. Applicable only on binary classification. (binary)</option>
0
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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="precision_score">
35
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161 <expand macro="clf_inputs" />
0
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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-->
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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165 <expand macro="pos_label" default_value="1" />
0
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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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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
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168 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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="recall_score">
35
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172 <expand macro="clf_inputs" />
0
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173 <section name="options" title="Advanced Options" expanded="False">
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174 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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175 <!--sample_weight-->
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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176 <expand macro="pos_label" default_value="1" />
0
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177 <expand macro="average">
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178 <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>
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179 </expand>
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180 </section>
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181 </when>
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182 <when value="zero_one_loss">
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183 <expand macro="clf_inputs" />
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184 <section name="options" title="Advanced Options" expanded="False">
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185 <!--sample_weight-->
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186 <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. " />
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187 </section>
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188 </when>
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189 <when value="auc">
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190 <expand macro="clf_inputs" />
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191 <section name="options" title="Advanced Options" expanded="False">
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192 <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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193 </section>
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194 </when>
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195 <when value="brier_score_loss">
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196 <expand macro="clf_inputs" />
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197 <section name="options" title="Advanced Options" expanded="False">
1
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198 <!--weights-->
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199 <expand macro="pos_label" />
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200 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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201 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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202 <when value="matthews_corrcoef">
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203 <expand macro="clf_inputs" />
1
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204 <!--section name="options" title="Advanced Options" expanded="False">
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205 </section-->
0
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206 </when>
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207 <when value="confusion_matrix">
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208 <expand macro="clf_inputs" />
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209 <!--section name="options" title="Advanced Options" expanded="False">
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210 <!- -labels- ->
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211 </section-->
0
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212 </when>
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213 <when value="precision_recall_curve">
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214 <expand macro="clf_inputs" />
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215 <section name="options" title="Advanced Options" expanded="False">
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216 <expand macro="pos_label" />
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217 <!--sample_weight-->
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218 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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219 </when>
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220 <when value="roc_curve">
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221 <expand macro="clf_inputs" />
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222 <section name="options" title="Advanced Options" expanded="False">
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223 <!--sample_weight-->
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224 <expand macro="pos_label" />
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225 <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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226 </section>
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227 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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228 <when value="hinge_loss">
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229 <expand macro="clf_inputs" multiple="true" />
1
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230 <!--section name="options" title="Advanced Options" expanded="False">
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231 <!- -labels- ->
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232 <!- -sample_weight- ->
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233 </section-->
0
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234 </when>
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235 <when value="log_loss">
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236 <expand macro="clf_inputs" multiple="true" />
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237 <section name="options" title="Advanced Options" expanded="False">
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238 <!--sample_weight-->
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239 <param argument="eps" type="float" value="1e-15" label="Clipping factor" 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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240 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" 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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241 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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242 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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243 <when value="average_precision_score">
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244 <expand macro="clf_inputs" multiple1="true" multiple="true" />
1
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245 <!-- section name="options" title="Advanced Options" expanded="False">
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246 <!- -average='macro', sample_weight=None- ->
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247 </section-->
0
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248 </when>
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249 <when value="roc_auc_score">
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250 <expand macro="clf_inputs" multiple1="true" multiple="true" />
0
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251 <section name="options" title="Advanced Options" expanded="False">
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252 <expand macro="average">
1
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253 <option value="macro" selected="true">Calculate metrics for each label, and find their unweighted mean. (macro)</option>
0
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254 </expand>
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255 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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256 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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257 </conditional>
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258 </inputs>
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259 <outputs>
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260 <data format="txt" name="outfile" />
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261 </outputs>
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262 <tests>
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263 <test>
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264 <param name="selected_metric" value="accuracy_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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parents: 32
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265 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
266 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
267 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
268 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
269 <output name="outfile" file="accuracy_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
270 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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271 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
272 <param name="selected_metric" value="classification_report" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
273 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
274 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
275 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
276 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
277 <output name="outfile" file="classification_report.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
278 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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279 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
280 <param name="selected_metric" value="f1_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
281 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
282 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
283 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
284 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
285 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
286 <output name="outfile" file="f1_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
287 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
288 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
289 <param name="selected_metric" value="fbeta_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
290 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
291 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
292 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
293 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
294 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
295 <output name="outfile" file="fbeta_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
296 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
297 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
298 <param name="selected_metric" value="hamming_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
299 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
300 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
301 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
302 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
303 <output name="outfile" file="hamming_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
304 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
305 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
306 <param name="selected_metric" value="jaccard_similarity_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
307 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
308 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
309 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
310 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
311 <output name="outfile" file="jaccard_similarity_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
312 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
313 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
314 <param name="selected_metric" value="precision_recall_fscore_support" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
315 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
316 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
317 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
318 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
319 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
320 <output name="outfile" file="precision_recall_fscore_support.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
321 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
322 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
323 <param name="selected_metric" value="precision_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
324 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
325 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
326 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
327 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
328 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
329 <output name="outfile" file="precision_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
330 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
331 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
332 <param name="selected_metric" value="recall_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
333 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
334 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
335 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
336 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
337 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
338 <output name="outfile" file="recall_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
339 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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340 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
341 <param name="selected_metric" value="zero_one_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
342 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
343 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
344 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
345 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
346 <output name="outfile" file="zero_one_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
347 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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348 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
349 <param name="selected_metric" value="auc" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
350 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
351 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
352 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
353 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
354 <param name="reorder" value="true" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
355 <output name="outfile" file="auc.txt" />
0
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
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diff changeset
357 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
358 <param name="selected_metric" value="brier_score_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
359 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
360 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
361 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
362 <param name="col2" value="4" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
363 <output name="outfile" file="brier_score_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
364 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
365 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
366 <param name="selected_metric" value="matthews_corrcoef" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
367 <param name="infile1" value="y.tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
368 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
369 <param name="infile2" value="y.tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
370 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
371 <output name="outfile" file="matthews_corrcoef.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
372 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
373 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
374 <param name="selected_metric" value="confusion_matrix" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
375 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
376 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
377 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
378 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
379 <output name="outfile" file="confusion_matrix.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
380 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
381 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
382 <param name="selected_metric" value="precision_recall_curve" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
383 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
384 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
385 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
386 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
387 <output name="outfile" file="precision_recall_curve.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
388 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
389 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
390 <param name="selected_metric" value="roc_curve" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
391 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
392 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
393 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
394 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
395 <output name="outfile" file="roc_curve.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
396 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
397 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
398 <param name="selected_metric" value="hinge_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
399 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
400 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
401 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
402 <param name="col2" value="8,9,10" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
403 <output name="outfile" file="hinge_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
404 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
405 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
406 <param name="selected_metric" value="log_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
407 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
408 <param name="col1" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
409 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
410 <param name="col2" value="3,4,5" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
411 <output name="outfile" file="log_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
412 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
413 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
414 <param name="selected_metric" value="average_precision_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
415 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
416 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
417 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
418 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
419 <output name="outfile" file="average_precision_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
420 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
421 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
422 <param name="selected_metric" value="roc_auc_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
423 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
424 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
425 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
426 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
427 <output name="outfile" file="roc_auc_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
428 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
429 </tests>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
430 <help>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
431 <![CDATA[
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
parents:
diff changeset
432 **What it does**
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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433 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on
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434 sklearn.metrics package.
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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435 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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436
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437 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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438 ]]>
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439 </help>
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440 <expand macro="sklearn_citation" />
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441 </tool>