Mercurial > repos > bgruening > sklearn_clf_metrics

annotate clf_metrics.xml @ 42:9fdff01a34b0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:37:34 +0000
parents ed7d6d7c6e93
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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>
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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
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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_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>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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95 </param>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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103 <when value="classification_report">
35
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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-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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107 <!--target_names-->
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108 <!--sample_weight-->
35
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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-->
35
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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>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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128 <!--sample_weight-->
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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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>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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135 <when value="hamming_loss">
35
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136 <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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137 <!--section name="options" title="Advanced Options" expanded="False">
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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138 <!- -classes- ->
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139 </section-->
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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140 </when>
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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141 <when value="jaccard_score">
35
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142 <expand macro="clf_inputs" />
0
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143 <section name="options" title="Advanced Options" expanded="False">
41
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diff changeset
144 <expand macro="average">
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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145 </expand>
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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146 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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147 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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148 <when value="precision_recall_fscore_support">
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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149 <expand macro="clf_inputs" />
0
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150 <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
151 <expand macro="beta" />
0
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 <!--warn_for-->
35
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155 <expand macro="pos_label" default_value="1" />
0
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156 <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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157 <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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158 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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159 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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160 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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161 <when value="precision_score">
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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162 <expand macro="clf_inputs" />
0
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163 <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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164 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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165 <!--sample_weight-->
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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166 <expand macro="pos_label" default_value="1" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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167 <expand macro="average">
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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168 <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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169 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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170 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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171 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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172 <when value="recall_score">
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
173 <expand macro="clf_inputs" />
0
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174 <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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175 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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176 <!--sample_weight-->
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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177 <expand macro="pos_label" default_value="1" />
0
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178 <expand macro="average">
1
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179 <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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180 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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181 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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182 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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183 <when value="zero_one_loss">
35
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184 <expand macro="clf_inputs" />
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185 <section name="options" title="Advanced Options" expanded="False">
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186 <!--sample_weight-->
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187 <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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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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188 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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189 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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190 <when value="auc">
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191 <expand macro="clf_inputs" />
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192 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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193 <when value="brier_score_loss">
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194 <expand macro="clf_inputs" />
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195 <section name="options" title="Advanced Options" expanded="False">
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196 <!--weights-->
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197 <expand macro="pos_label" />
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198 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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199 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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200 <when value="matthews_corrcoef">
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201 <expand macro="clf_inputs" />
1
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202 <!--section name="options" title="Advanced Options" expanded="False">
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203 </section-->
0
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204 </when>
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205 <when value="confusion_matrix">
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206 <expand macro="clf_inputs" />
1
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207 <!--section name="options" title="Advanced Options" expanded="False">
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208 <!- -labels- ->
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209 </section-->
0
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210 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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211 <when value="precision_recall_curve">
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212 <expand macro="clf_inputs" />
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213 <section name="options" title="Advanced Options" expanded="False">
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214 <expand macro="pos_label" />
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215 <!--sample_weight-->
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216 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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217 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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218 <when value="roc_curve">
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219 <expand macro="clf_inputs" />
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220 <section name="options" title="Advanced Options" expanded="False">
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221 <!--sample_weight-->
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222 <expand macro="pos_label" />
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223 <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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224 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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225 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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226 <when value="hinge_loss">
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227 <expand macro="clf_inputs" multiple="true" />
1
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228 <!--section name="options" title="Advanced Options" expanded="False">
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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229 <!- -labels- ->
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230 <!- -sample_weight- ->
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231 </section-->
0
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232 </when>
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233 <when value="log_loss">
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234 <expand macro="clf_inputs" multiple="true" />
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235 <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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236 <!--sample_weight-->
35
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237 <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)). " />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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238 <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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239 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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240 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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241 <when value="average_precision_score">
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242 <expand macro="clf_inputs" multiple1="true" multiple="true" />
1
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243 <!-- section name="options" title="Advanced Options" expanded="False">
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244 <!- -average='macro', sample_weight=None- ->
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245 </section-->
0
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246 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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247 <when value="roc_auc_score">
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248 <expand macro="clf_inputs" multiple1="true" multiple="true" />
0
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249 <section name="options" title="Advanced Options" expanded="False">
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250 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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251 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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252 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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253 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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254 </conditional>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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255 </inputs>
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256 <outputs>
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257 <data format="txt" name="outfile" />
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258 </outputs>
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259 <tests>
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260 <test>
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261 <param name="selected_metric" value="accuracy_score" />
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262 <param name="infile1" value="y.tabular" ftype="tabular" />
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263 <param name="col1" value="1" />
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264 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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265 <param name="col2" value="2" />
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266 <output name="outfile" file="accuracy_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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267 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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268 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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269 <param name="selected_metric" value="classification_report" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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270 <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
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271 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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272 <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
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273 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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274 <output name="outfile" file="classification_report.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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275 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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276 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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277 <param name="selected_metric" value="f1_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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278 <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
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279 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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280 <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
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281 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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282 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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283 <output name="outfile" file="f1_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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284 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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285 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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286 <param name="selected_metric" value="fbeta_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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287 <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
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288 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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289 <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
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290 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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291 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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292 <output name="outfile" file="fbeta_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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293 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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294 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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295 <param name="selected_metric" value="hamming_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
296 <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
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diff changeset
297 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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298 <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
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299 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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300 <output name="outfile" file="hamming_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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301 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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302 <test>
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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303 <param name="selected_metric" value="jaccard_score" />
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
304 <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
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diff changeset
305 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
306 <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
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diff changeset
307 <param name="col2" value="2" />
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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diff changeset
308 <param name="average" value="weighted" />
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
309 <output name="outfile" file="jaccard_similarity_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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310 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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311 <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
312 <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
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diff changeset
313 <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
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diff changeset
314 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
315 <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
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diff changeset
316 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
317 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
318 <output name="outfile" file="precision_recall_fscore_support.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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319 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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320 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 32
diff changeset
321 <param name="selected_metric" value="precision_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
322 <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
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diff changeset
323 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
324 <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
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diff changeset
325 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
326 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
327 <output name="outfile" file="precision_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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328 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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329 <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
330 <param name="selected_metric" value="recall_score" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
331 <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
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diff changeset
332 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
333 <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
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diff changeset
334 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
335 <param name="average" value="micro" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
336 <output name="outfile" file="recall_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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337 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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338 <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
339 <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
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diff changeset
340 <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
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diff changeset
341 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
342 <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
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diff changeset
343 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
344 <output name="outfile" file="zero_one_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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345 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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346 <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
347 <param name="selected_metric" value="auc" />
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
348 <param name="infile1" value="y_sorted.tabular" ftype="tabular" />
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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349 <param name="col1" value="1" />
41
ed7d6d7c6e93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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350 <param name="infile2" value="y_sorted.tabular" ftype="tabular" />
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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351 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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352 <output name="outfile" file="auc.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
353 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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354 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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355 <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
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diff changeset
356 <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
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357 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
358 <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
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diff changeset
359 <param name="col2" value="4" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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360 <output name="outfile" file="brier_score_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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361 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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362 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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363 <param name="selected_metric" value="matthews_corrcoef" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
364 <param name="infile1" value="y.tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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365 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
366 <param name="infile2" value="y.tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
367 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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368 <output name="outfile" file="matthews_corrcoef.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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369 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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370 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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371 <param name="selected_metric" value="confusion_matrix" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
372 <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
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diff changeset
373 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
374 <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
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diff changeset
375 <param name="col2" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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376 <output name="outfile" file="confusion_matrix.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
377 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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378 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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diff changeset
379 <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
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diff changeset
380 <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
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diff changeset
381 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
382 <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
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383 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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384 <output name="outfile" file="precision_recall_curve.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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385 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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386 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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387 <param name="selected_metric" value="roc_curve" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
388 <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
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diff changeset
389 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
390 <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
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diff changeset
391 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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392 <output name="outfile" file="roc_curve.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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diff changeset
393 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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394 <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
395 <param name="selected_metric" value="hinge_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
396 <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
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diff changeset
397 <param name="col1" value="1" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
398 <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
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diff changeset
399 <param name="col2" value="8,9,10" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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400 <output name="outfile" file="hinge_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
401 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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402 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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403 <param name="selected_metric" value="log_loss" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
404 <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
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diff changeset
405 <param name="col1" value="2" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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406 <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
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407 <param name="col2" value="3,4,5" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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408 <output name="outfile" file="log_loss.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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diff changeset
409 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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410 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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411 <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
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diff changeset
412 <param name="infile1" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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413 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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414 <param name="infile2" value="y.tabular" ftype="tabular" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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415 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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416 <output name="outfile" file="average_precision_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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417 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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418 <test>
35
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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419 <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
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diff changeset
420 <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
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diff changeset
421 <param name="col1" value="6" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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diff changeset
422 <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
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diff changeset
423 <param name="col2" value="7" />
3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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424 <output name="outfile" file="roc_auc_score.txt" />
0
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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425 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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426 </tests>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
bgruening
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427 <help>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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428 <![CDATA[
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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429 **What it does**
1
65bd390f50ae planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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430 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
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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431 sklearn.metrics package.
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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432 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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433
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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434 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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435 ]]>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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436 </help>
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3c5034b0d775 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
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437 <expand macro="sklearn_citation" />
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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438 </tool>