sklearn_clf_metrics: clf_metrics.xml annotate

author	bgruening
date	Thu, 23 Jun 2016 15:26:39 -0400
parents
children	65bd390f50ae

rev	line source
0 8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	2 <description>for classification performance</description>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	3 <macros>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	4 <import>main_macros.xml</import>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	5 </macros>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	6 <expand macro="python_requirements"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	7 <expand macro="macro_stdio"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	8 <version_command>echo "@VERSION@"</version_command>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	9 <command>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	10 <![CDATA[
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	11 python "$clf_metrics_script" '$inputs'
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	12 ]]>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	13 </command>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	14 <configfiles>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	15 <inputs name="inputs" />
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	16 <configfile name="clf_metrics_script">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	17 <![CDATA[
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	18 import sys
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	19 import json
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	20 import pandas
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	21 import numpy as np
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	22 from sklearn import metrics
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	23
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	24 @COLUMNS_FUNCTION@
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	25
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	26 input_json_path = sys.argv[1]
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	27 params = json.load(open(input_json_path, "r"))
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	28
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	29
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	30 y_t = columns("$clf_metrics.infile1","$clf_metrics.col1")
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	31 y_p = columns("$clf_metrics.infile2","$clf_metrics.col2")
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	32
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	33 options = params["clf_metrics"]["options"]
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	34 metric = params["clf_metrics"]["selected_metric"]
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	35 metric_function = getattr(metrics, metric)
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	36 res = metric_function(y_t,y_p,**options)
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	37 with open("$outfile", 'w+') as out_file:
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	38 out_file.write( metric + ' : ' + '\n' + str(res) + '\n' )
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	39
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	40 ]]>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	41 </configfile>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	42 </configfiles>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	43 <inputs>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	44 <conditional name="clf_metrics">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	45 <param name="selected_metric" type="select" label="Metrics">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	46 <option value="accuracy_score" selected="true">Accuracy classification score</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	47 <option value="classification_report">Text report of the main classification metrics</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	48 <option value="f1_score">F1 score (aka balanced F-score or F-measure)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	49 <option value="fbeta_score">F-beta score</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	50 <option value="hamming_loss">Average Hamming loss</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	51 <option value="jaccard_similarity_score">Jaccard similarity coefficient score</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	52 <option value="precision_recall_fscore_support">Compute precision, recall, F-measure and support for each class</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	53 <option value="precision_score">Precision</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	54 <option value="recall_score">Recall</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	55 <option value="zero_one_loss">Zero-one classification loss</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	56 <option value="auc">Area under the curve (AUC)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	57 <option value="brier_score_loss">Brier score</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	58 <option value="matthews_corrcoef">Matthews correlation coefficient (MCC) for binary classes</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	59 <option value="confusion_matrix">Confusion matrix (evaluate the accuracy of a classification)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	60 <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 bgruening parents: diff changeset	61 <option value="roc_curve">Receiver operating characteristic (ROC)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	62 <option value="hinge_loss">Average hinge loss (non-regularized)</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	63 <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 bgruening parents: diff changeset	64 <option value="average_precision_score">Average precision (AP) from prediction scores</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	65 <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 bgruening parents: diff changeset	66 </param>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	67 <when value="accuracy_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	68 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	69 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	70 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	71 <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. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	72 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	73 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	74 <when value="classification_report">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	75 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	76 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	77 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	78 <!--target_names-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	79 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	80 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help=""/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	81 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	82 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	83 <when value="f1_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	84 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	85 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	86 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	87 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	88 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	89 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	90 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary.">binary</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	91 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	92 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	93 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	94 <when value="fbeta_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	95 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	96 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	97 <expand macro="beta"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	98 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	99 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	100 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	101 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	102 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary.">binary</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	103 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	104 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	105 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	106 <when value="hamming_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	107 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	108 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	109 <!--classes-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	110 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	111 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	112 <when value="jaccard_similarity_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	113 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	114 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	115 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	116 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	117 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	118 <when value="precision_recall_fscore_support">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	119 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	120 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	121 <expand macro="beta"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	122 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	123 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	124 <!--warn_for-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	125 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	126 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	127 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. Applicable only on binary classification.">binary</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	128 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	129 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	130 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	131 <when value="precision_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	132 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	133 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	134 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	135 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	136 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	137 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	138 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary.">binary</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	139 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	140 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	141 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	142 <when value="recall_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	143 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	144 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	145 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	146 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	147 <expand macro="pos_label" default_value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	148 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	149 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary.">binary</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	150 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	151 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	152 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	153 <when value="zero_one_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	154 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	155 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	156 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	157 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	158 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	159 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	160 <when value="auc">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	161 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	162 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	163 <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. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	164 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	165 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	166 <when value="brier_score_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	167 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	168 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	169 <!--weights-->>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	170 <expand macro="pos_label"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	171 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	172 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	173 <when value="matthews_corrcoef">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	174 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	175 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	176 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	177 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	178 <when value="confusion_matrix">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	179 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	180 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	181 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	182 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	183 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	184 <when value="precision_recall_curve">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	185 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	186 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	187 <expand macro="pos_label"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	188 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	189 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	190 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	191 <when value="roc_curve">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	192 <expand macro="clf_inputs"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	193 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	194 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	195 <expand macro="pos_label"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	196 <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. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	197 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	198 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	199 <when value="hinge_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	200 <expand macro="clf_inputs" multiple="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	201 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	202 <!--labels-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	203 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	204 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	205 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	206 <when value="log_loss">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	207 <expand macro="clf_inputs" multiple="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	208 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	209 <!--sample_weight-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	210 <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)). "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	211 <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. "/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	212 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	213 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	214 <when value="average_precision_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	215 <expand macro="clf_inputs" multiple1="true" multiple="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	216 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	217 <!--average='macro', sample_weight=None-->
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	218 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	219 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	220 <when value="roc_auc_score">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	221 <expand macro="clf_inputs" multiple1="true" multiple="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	222 <section name="options" title="Advanced Options" expanded="False">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	223 <expand macro="average">
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	224 <option value="macro" selected="true" help="Calculate metrics for each label, and find their unweighted mean.">macro</option>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	225 </expand>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	226 </section>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	227 </when>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	228 </conditional>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	229 </inputs>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	230 <outputs>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	231 <data format="txt" name="outfile"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	232 </outputs>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	233 <tests>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	234 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	235 <param name="selected_metric" value="accuracy_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	236 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	237 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	238 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	239 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	240 <output name="outfile" file="accuracy_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	241 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	242 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	243 <param name="selected_metric" value="classification_report"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	244 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	245 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	246 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	247 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	248 <output name="outfile" file="classification_report.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	249 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	250 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	251 <param name="selected_metric" value="f1_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	252 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	253 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	254 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	255 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	256 <param name="average" value="binary"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	257 <output name="outfile" file="f1_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	258 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	259 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	260 <param name="selected_metric" value="fbeta_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	261 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	262 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	263 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	264 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	265 <output name="outfile" file="fbeta_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	266 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	267 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	268 <param name="selected_metric" value="hamming_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	269 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	270 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	271 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	272 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	273 <output name="outfile" file="hamming_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	274 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	275 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	276 <param name="selected_metric" value="jaccard_similarity_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	277 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	278 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	279 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	280 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	281 <output name="outfile" file="jaccard_similarity_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	282 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	283 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	284 <param name="selected_metric" value="precision_recall_fscore_support"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	285 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	286 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	287 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	288 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	289 <output name="outfile" file="precision_recall_fscore_support.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	290 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	291 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	292 <param name="selected_metric" value="precision_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	293 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	294 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	295 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	296 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	297 <output name="outfile" file="precision_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	298 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	299 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	300 <param name="selected_metric" value="recall_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	301 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	302 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	303 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	304 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	305 <output name="outfile" file="recall_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	306 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	307 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	308 <param name="selected_metric" value="zero_one_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	309 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	310 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	311 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	312 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	313 <output name="outfile" file="zero_one_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	314 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	315 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	316 <param name="selected_metric" value="auc"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	317 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	318 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	319 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	320 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	321 <param name="reorder" value="true"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	322 <output name="outfile" file="auc.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	323 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	324 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	325 <param name="selected_metric" value="brier_score_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	326 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	327 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	328 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	329 <param name="col2" value="3"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	330 <output name="outfile" file="brier_score_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	331 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	332 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	333 <param name="selected_metric" value="matthews_corrcoef"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	334 <param name="infile1" value="y.tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	335 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	336 <param name="infile2" value="y.tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	337 <param name="col2" value="7"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	338 <output name="outfile" file="matthews_corrcoef.txt"/>
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 parents: diff changeset	340 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	341 <param name="selected_metric" value="confusion_matrix"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	342 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	343 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	344 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	345 <param name="col2" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	346 <output name="outfile" file="confusion_matrix.txt"/>
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 parents: diff changeset	348 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	349 <param name="selected_metric" value="precision_recall_curve"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	350 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	351 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	352 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	353 <param name="col2" value="7"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	354 <output name="outfile" file="precision_recall_curve.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	355 </test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	356 <test>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	357 <param name="selected_metric" value="roc_curve"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	358 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	359 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	360 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	361 <param name="col2" value="7"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	362 <output name="outfile" file="roc_curve.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	363 </test>
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 <param name="selected_metric" value="hinge_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	366 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	367 <param name="col1" value="1"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	368 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	369 <param name="col2" value="8,9,10"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	370 <output name="outfile" file="hinge_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	371 </test>
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 <param name="selected_metric" value="log_loss"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	374 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	375 <param name="col1" value="2"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	376 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	377 <param name="col2" value="3,4,5"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	378 <output name="outfile" file="log_loss.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	379 </test>
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 parents: diff changeset	381 <param name="selected_metric" value="average_precision_score"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	382 <param name="infile1" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	383 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	384 <param name="infile2" value="y.tabular" ftype="tabular"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	385 <param name="col2" value="7"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	386 <output name="outfile" file="average_precision_score.txt"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	387 </test>
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	389 <param name="selected_metric" value="roc_auc_score"/>
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	391 <param name="col1" value="6"/>
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	392 <param name="infile2" value="y.tabular" ftype="tabular"/>
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	399 What it does
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	400 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
8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	401 sklearn.metrics package.
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8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991 bgruening parents: diff changeset	405 ]]>
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0

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1 <tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@">

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2 <description>for classification performance</description>

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3 <macros>

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4 <import>main_macros.xml</import>

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5 </macros>

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6 <expand macro="python_requirements"/>

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7 <expand macro="macro_stdio"/>

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8 <version_command>echo "@VERSION@"</version_command>

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9 <command>

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10 <![CDATA[

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11 python "$clf_metrics_script" '$inputs'

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12 ]]>

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13 </command>

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14 <configfiles>

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15 <inputs name="inputs" />

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16 <configfile name="clf_metrics_script">

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17 <![CDATA[

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18 import sys

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19 import json

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20 import pandas

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21 import numpy as np

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22 from sklearn import metrics

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23

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24 @COLUMNS_FUNCTION@

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25

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26 input_json_path = sys.argv[1]

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27 params = json.load(open(input_json_path, "r"))

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28

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29

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30 y_t = columns("$clf_metrics.infile1","$clf_metrics.col1")

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31 y_p = columns("$clf_metrics.infile2","$clf_metrics.col2")

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32

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33 options = params["clf_metrics"]["options"]

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34 metric = params["clf_metrics"]["selected_metric"]

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35 metric_function = getattr(metrics, metric)

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36 res = metric_function(y_t,y_p,**options)

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37 with open("$outfile", 'w+') as out_file:

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38 out_file.write( metric + ' : ' + '\n' + str(res) + '\n' )

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39

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40 ]]>

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41 </configfile>

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42 </configfiles>

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43 <inputs>

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44 <conditional name="clf_metrics">

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45 <param name="selected_metric" type="select" label="Metrics">

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46 <option value="accuracy_score" selected="true">Accuracy classification score</option>

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47 <option value="classification_report">Text report of the main classification metrics</option>

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48 <option value="f1_score">F1 score (aka balanced F-score or F-measure)</option>

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49 <option value="fbeta_score">F-beta score</option>

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50 <option value="hamming_loss">Average Hamming loss</option>

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51 <option value="jaccard_similarity_score">Jaccard similarity coefficient score</option>

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52 <option value="precision_recall_fscore_support">Compute precision, recall, F-measure and support for each class</option>

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53 <option value="precision_score">Precision</option>

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54 <option value="recall_score">Recall</option>

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55 <option value="zero_one_loss">Zero-one classification loss</option>

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56 <option value="auc">Area under the curve (AUC)</option>

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57 <option value="brier_score_loss">Brier score</option>

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58 <option value="matthews_corrcoef">Matthews correlation coefficient (MCC) for binary classes</option>

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59 <option value="confusion_matrix">Confusion matrix (evaluate the accuracy of a classification)</option>

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60 <option value="precision_recall_curve">Precision-recall pairs for different probability thresholds</option>

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61 <option value="roc_curve">Receiver operating characteristic (ROC)</option>

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62 <option value="hinge_loss">Average hinge loss (non-regularized)</option>

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63 <option value="log_loss">Log loss (aka logistic loss or cross-entropy loss)</option>

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64 <option value="average_precision_score">Average precision (AP) from prediction scores</option>

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65 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option>

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66 </param>

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67 <when value="accuracy_score">

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68 <expand macro="clf_inputs"/>

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69 <section name="options" title="Advanced Options" expanded="False">

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70

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71 <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. "/>

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72 </section>

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73 </when>

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74 <when value="classification_report">

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75 <expand macro="clf_inputs"/>

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76 <section name="options" title="Advanced Options" expanded="False">

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77

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78

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79

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80 <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help=""/>

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81 </section>

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82 </when>

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83 <when value="f1_score">

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84 <expand macro="clf_inputs"/>

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85 <section name="options" title="Advanced Options" expanded="False">

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86

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87

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88 <expand macro="pos_label" default_value="1"/>

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89 <expand macro="average">

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90 <option value="binary" selected="true" help="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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91 </expand>

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92 </section>

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93 </when>

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94 <when value="fbeta_score">

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95 <expand macro="clf_inputs"/>

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96 <section name="options" title="Advanced Options" expanded="False">

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97 <expand macro="beta"/>

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98

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99

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100 <expand macro="pos_label" default_value="1"/>

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101 <expand macro="average">

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102 <option value="binary" selected="true" help="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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103 </expand>

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104 </section>

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105 </when>

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106 <when value="hamming_loss">

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107 <expand macro="clf_inputs"/>

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108 <section name="options" title="Advanced Options" expanded="False">

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109

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110 </section>

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111 </when>

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112 <when value="jaccard_similarity_score">

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113 <expand macro="clf_inputs"/>

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114 <section name="options" title="Advanced Options" expanded="False">

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115 <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. "/>

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116 </section>

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117 </when>

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118 <when value="precision_recall_fscore_support">

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119 <expand macro="clf_inputs"/>

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120 <section name="options" title="Advanced Options" expanded="False">

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121 <expand macro="beta"/>

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122

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123

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124

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125 <expand macro="pos_label" default_value="1"/>

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126 <expand macro="average">

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127 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. Applicable only on binary classification.">binary</option>

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128 </expand>

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129 </section>

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130 </when>

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131 <when value="precision_score">

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132 <expand macro="clf_inputs"/>

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133 <section name="options" title="Advanced Options" expanded="False">

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134

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135

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136 <expand macro="pos_label" default_value="1"/>

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137 <expand macro="average">

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138 <option value="binary" selected="true" help="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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139 </expand>

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140 </section>

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141 </when>

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142 <when value="recall_score">

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143 <expand macro="clf_inputs"/>

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144 <section name="options" title="Advanced Options" expanded="False">

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145

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146

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147 <expand macro="pos_label" default_value="1"/>

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148 <expand macro="average">

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149 <option value="binary" selected="true" help="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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150 </expand>

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151 </section>

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152 </when>

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153 <when value="zero_one_loss">

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154 <expand macro="clf_inputs"/>

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155 <section name="options" title="Advanced Options" expanded="False">

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156

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157 <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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158 </section>

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159 </when>

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160 <when value="auc">

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161 <expand macro="clf_inputs"/>

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162 <section name="options" title="Advanced Options" expanded="False">

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163 <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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164 </section>

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165 </when>

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166 <when value="brier_score_loss">

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167 <expand macro="clf_inputs"/>

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168 <section name="options" title="Advanced Options" expanded="False">

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169 >

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170 <expand macro="pos_label"/>

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171 </section>

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172 </when>

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173 <when value="matthews_corrcoef">

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174 <expand macro="clf_inputs"/>

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175 <section name="options" title="Advanced Options" expanded="False">

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176 </section>

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177 </when>

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178 <when value="confusion_matrix">

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179 <expand macro="clf_inputs"/>

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180 <section name="options" title="Advanced Options" expanded="False">

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181

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182 </section>

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183 </when>

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184 <when value="precision_recall_curve">

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185 <expand macro="clf_inputs"/>

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186 <section name="options" title="Advanced Options" expanded="False">

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187 <expand macro="pos_label"/>

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188

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189 </section>

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190 </when>

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191 <when value="roc_curve">

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192 <expand macro="clf_inputs"/>

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193 <section name="options" title="Advanced Options" expanded="False">

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194

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195 <expand macro="pos_label"/>

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196 <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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197 </section>

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198 </when>

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199 <when value="hinge_loss">

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200 <expand macro="clf_inputs" multiple="true"/>

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201 <section name="options" title="Advanced Options" expanded="False">

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202

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203

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204 </section>

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205 </when>

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206 <when value="log_loss">

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207 <expand macro="clf_inputs" multiple="true"/>

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208 <section name="options" title="Advanced Options" expanded="False">

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209

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210 <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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211 <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. "/>

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212 </section>

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213 </when>

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214 <when value="average_precision_score">

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215 <expand macro="clf_inputs" multiple1="true" multiple="true"/>

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216 <section name="options" title="Advanced Options" expanded="False">

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217

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218 </section>

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219 </when>

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220 <when value="roc_auc_score">

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221 <expand macro="clf_inputs" multiple1="true" multiple="true"/>

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222 <section name="options" title="Advanced Options" expanded="False">

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223 <expand macro="average">

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224 <option value="macro" selected="true" help="Calculate metrics for each label, and find their unweighted mean.">macro</option>

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225 </expand>

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226 </section>

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227 </when>

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228 </conditional>

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229 </inputs>

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230 <outputs>

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231 <data format="txt" name="outfile"/>

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232 </outputs>

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233 <tests>

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234 <test>

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235 <param name="selected_metric" value="accuracy_score"/>

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236 <param name="infile1" value="y.tabular" ftype="tabular"/>

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237 <param name="col1" value="1"/>

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238 <param name="infile2" value="y.tabular" ftype="tabular"/>

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239 <param name="col2" value="2"/>

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240 <output name="outfile" file="accuracy_score.txt"/>

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241 </test>

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242 <test>

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243 <param name="selected_metric" value="classification_report"/>

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244 <param name="infile1" value="y.tabular" ftype="tabular"/>

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245 <param name="col1" value="1"/>

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246 <param name="infile2" value="y.tabular" ftype="tabular"/>

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247 <param name="col2" value="2"/>

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248 <output name="outfile" file="classification_report.txt"/>

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249 </test>

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250 <test>

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251 <param name="selected_metric" value="f1_score"/>

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252 <param name="infile1" value="y.tabular" ftype="tabular"/>

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253 <param name="col1" value="1"/>

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254 <param name="infile2" value="y.tabular" ftype="tabular"/>

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255 <param name="col2" value="2"/>

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256 <param name="average" value="binary"/>

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257 <output name="outfile" file="f1_score.txt"/>

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258 </test>

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259 <test>

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260 <param name="selected_metric" value="fbeta_score"/>

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261 <param name="infile1" value="y.tabular" ftype="tabular"/>

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262 <param name="col1" value="1"/>

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263 <param name="infile2" value="y.tabular" ftype="tabular"/>

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264 <param name="col2" value="2"/>

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265 <output name="outfile" file="fbeta_score.txt"/>

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266 </test>

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267 <test>

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268 <param name="selected_metric" value="hamming_loss"/>

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269 <param name="infile1" value="y.tabular" ftype="tabular"/>

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270 <param name="col1" value="1"/>

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271 <param name="infile2" value="y.tabular" ftype="tabular"/>

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272 <param name="col2" value="2"/>

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273 <output name="outfile" file="hamming_loss.txt"/>

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274 </test>

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275 <test>

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276 <param name="selected_metric" value="jaccard_similarity_score"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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277 <param name="infile1" value="y.tabular" ftype="tabular"/>

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278 <param name="col1" value="1"/>

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279 <param name="infile2" value="y.tabular" ftype="tabular"/>

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280 <param name="col2" value="2"/>

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281 <output name="outfile" file="jaccard_similarity_score.txt"/>

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282 </test>

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283 <test>

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284 <param name="selected_metric" value="precision_recall_fscore_support"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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285 <param name="infile1" value="y.tabular" ftype="tabular"/>

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286 <param name="col1" value="1"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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287 <param name="infile2" value="y.tabular" ftype="tabular"/>

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288 <param name="col2" value="2"/>

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289 <output name="outfile" file="precision_recall_fscore_support.txt"/>

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290 </test>

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291 <test>

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292 <param name="selected_metric" value="precision_score"/>

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293 <param name="infile1" value="y.tabular" ftype="tabular"/>

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294 <param name="col1" value="1"/>

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295 <param name="infile2" value="y.tabular" ftype="tabular"/>

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296 <param name="col2" value="2"/>

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297 <output name="outfile" file="precision_score.txt"/>

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298 </test>

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299 <test>

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300 <param name="selected_metric" value="recall_score"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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301 <param name="infile1" value="y.tabular" ftype="tabular"/>

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302 <param name="col1" value="1"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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303 <param name="infile2" value="y.tabular" ftype="tabular"/>

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304 <param name="col2" value="2"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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305 <output name="outfile" file="recall_score.txt"/>

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306 </test>

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307 <test>

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diff changeset

308 <param name="selected_metric" value="zero_one_loss"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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309 <param name="infile1" value="y.tabular" ftype="tabular"/>

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diff changeset

310 <param name="col1" value="1"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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311 <param name="infile2" value="y.tabular" ftype="tabular"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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312 <param name="col2" value="2"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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313 <output name="outfile" file="zero_one_loss.txt"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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314 </test>

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315 <test>

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316 <param name="selected_metric" value="auc"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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317 <param name="infile1" value="y.tabular" ftype="tabular"/>

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318 <param name="col1" value="1"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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319 <param name="infile2" value="y.tabular" ftype="tabular"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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320 <param name="col2" value="2"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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321 <param name="reorder" value="true"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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322 <output name="outfile" file="auc.txt"/>

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323 </test>

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324 <test>

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325 <param name="selected_metric" value="brier_score_loss"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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326 <param name="infile1" value="y.tabular" ftype="tabular"/>

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327 <param name="col1" value="1"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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328 <param name="infile2" value="y.tabular" ftype="tabular"/>

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329 <param name="col2" value="3"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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330 <output name="outfile" file="brier_score_loss.txt"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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331 </test>

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332 <test>

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333 <param name="selected_metric" value="matthews_corrcoef"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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334 <param name="infile1" value="y.tabular"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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335 <param name="col1" value="6"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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336 <param name="infile2" value="y.tabular"/>

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337 <param name="col2" value="7"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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338 <output name="outfile" file="matthews_corrcoef.txt"/>

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339 </test>

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340 <test>

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341 <param name="selected_metric" value="confusion_matrix"/>

8d7f8dc7c347 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

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342 <param name="infile1" value="y.tabular" ftype="tabular"/>

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343 <param name="col1" value="1"/>

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344 <param name="infile2" value="y.tabular" ftype="tabular"/>

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345 <param name="col2" value="2"/>

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346 <output name="outfile" file="confusion_matrix.txt"/>

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347 </test>

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348 <test>

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349 <param name="selected_metric" value="precision_recall_curve"/>

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350 <param name="infile1" value="y.tabular" ftype="tabular"/>

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351 <param name="col1" value="6"/>

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352 <param name="infile2" value="y.tabular" ftype="tabular"/>

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353 <param name="col2" value="7"/>

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354 <output name="outfile" file="precision_recall_curve.txt"/>

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355 </test>

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356 <test>

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357 <param name="selected_metric" value="roc_curve"/>

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358 <param name="infile1" value="y.tabular" ftype="tabular"/>

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359 <param name="col1" value="6"/>

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360 <param name="infile2" value="y.tabular" ftype="tabular"/>

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361 <param name="col2" value="7"/>

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362 <output name="outfile" file="roc_curve.txt"/>

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363 </test>

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364 <test>

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365 <param name="selected_metric" value="hinge_loss"/>

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366 <param name="infile1" value="y.tabular" ftype="tabular"/>

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367 <param name="col1" value="1"/>

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368 <param name="infile2" value="y.tabular" ftype="tabular"/>

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369 <param name="col2" value="8,9,10"/>

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370 <output name="outfile" file="hinge_loss.txt"/>

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371 </test>

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372 <test>

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373 <param name="selected_metric" value="log_loss"/>

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374 <param name="infile1" value="y.tabular" ftype="tabular"/>

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375 <param name="col1" value="2"/>

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376 <param name="infile2" value="y.tabular" ftype="tabular"/>

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377 <param name="col2" value="3,4,5"/>

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378 <output name="outfile" file="log_loss.txt"/>

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379 </test>

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380 <test>

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381 <param name="selected_metric" value="average_precision_score"/>

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382 <param name="infile1" value="y.tabular" ftype="tabular"/>

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383 <param name="col1" value="6"/>

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384 <param name="infile2" value="y.tabular" ftype="tabular"/>

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385 <param name="col2" value="7"/>

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386 <output name="outfile" file="average_precision_score.txt"/>

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387 </test>

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388 <test>

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389 <param name="selected_metric" value="roc_auc_score"/>

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390 <param name="infile1" value="y.tabular" ftype="tabular"/>

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391 <param name="col1" value="6"/>

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392 <param name="infile2" value="y.tabular" ftype="tabular"/>

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393 <param name="col2" value="7"/>

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394 <output name="outfile" file="roc_auc_score.txt"/>

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395 </test>

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396 </tests>

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397 <help>

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398 <![CDATA[

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399 **What it does**

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400 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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401 sklearn.metrics package.

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402 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.

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403

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404 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics

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405 ]]>

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406 </help>

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407 <expand macro="sklearn_citation"/>

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408 </tool>

Mercurial > repos > bgruening > sklearn_clf_metrics

annotate clf_metrics.xml @ 0:8d7f8dc7c347 draft