Mercurial > repos > bgruening > plotly_ml_performance_plots

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
author bgruening
date Thu, 11 Oct 2018 14:37:28 -0400
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children 2cfa4aabda3e
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c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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1 <tool id="plotly_ml_performance_plots" name="Plot confusion matrix, precision, recall and ROC and AUC curves" version="0.1">
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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2 <description>of tabular data</description>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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3 <requirements>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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4 <requirement type="package" version="0.22.0">pandas</requirement>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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5 <requirement type="package" version="3.1.1">plotly</requirement>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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6 <requirement type="package" version="0.19.1">scikit-learn</requirement>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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7 <requirement type="package" version="1.1.0">scipy</requirement>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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8 </requirements>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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9 <version_command>echo $version</version_command>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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10 <command detect_errors="aggressive"><![CDATA[
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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11 python '$__tool_directory__/plot_ml_performance.py'
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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12 -i '$infile_input'
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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13 -j '$infile_output'
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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14 -k '$infile_trained_model'
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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15 ]]>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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16 </command>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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17 <inputs>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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18 <param name="infile_input" type="data" format="tabular" label="Select input data file :" help="Input data is a matrix (tabular) where each column is a feature and the last column contains the (true or original) class labels."/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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19 <param name="infile_output" type="data" format="tabular" label="Select predicted data file :" help="Predicted data is a matrix (tabular) where each column is a feature and the last column contains the predicted class labels."/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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20 <param name="infile_trained_model" type="data" format="zip" label="Select trained model :" help="This file is a final model trained on training data."/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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21 </inputs>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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22
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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23 <outputs>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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24 <data name="output_confusion" format="html" from_work_dir="output_confusion.html" label="Confusion matrix of tabular data on ${on_string}"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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25 <data name="output_prf" format="html" from_work_dir="output_prf.html" label="Precision, recall and f-score of tabular data on ${on_string}"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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26 <data name="output_roc" format="html" from_work_dir="output_roc.html" label="ROC and AUC curves of tabular data on ${on_string}"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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27 </outputs>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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29 <tests>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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30 <test>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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31 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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32 <param name="infile_output" value="binary_prediction_sgd.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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33 <param name="infile_trained_model" value="model_binary_sgd.zip" ftype="zip"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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34 <output name="output_confusion" file="cnf_binary_sgd.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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35 <output name="output_prf" file="prf_binary_sgd.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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36 <output name="output_roc" file="roc_auc_binary_sgd.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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37 </test>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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38
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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39 <test>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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40 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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41 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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42 <param name="infile_trained_model" value="model_binary_linearsvm.zip" ftype="zip"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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43 <output name="output_confusion" file="cnf_binary_linearsvm.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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44 <output name="output_prf" file="prf_binary_linearsvm.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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45 <output name="output_roc" file="roc_auc_binary_linearsvm.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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46 </test>
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47
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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48 <test>
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49 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
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50 <param name="infile_output" value="prediction_binary_rfc.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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51 <param name="infile_trained_model" value="model_binary_rfc.zip" ftype="zip"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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52 <output name="output_confusion" file="cnf_binary_rfc.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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53 <output name="output_prf" file="prf_binary_rfc.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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54 <output name="output_roc" file="roc_auc_binary_rfc.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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55 </test>
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56
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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57 <test>
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58 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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59 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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60 <param name="infile_trained_model" value="model_binary_knn.zip" ftype="zip"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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61 <output name="output_confusion" file="cnf_binary_knn.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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62 <output name="output_prf" file="prf_binary_knn.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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63 <output name="output_roc" file="roc_auc_binary_knn.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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64 </test>
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65
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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66 <test>
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67 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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68 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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69 <param name="infile_trained_model" value="model_multi_lr.zip" ftype="zip"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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70 <output name="output_confusion" file="cnf_multi_lr.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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71 <output name="output_prf" file="prf_multi_lr.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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72 <output name="output_roc" file="roc_auc_multi_lr.html" compare="sim_size"/>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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73 </test>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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74
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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75 </tests>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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76 <help><![CDATA[
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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77 **What it does**
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c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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80 Produce a `heatmap plot (confusion matrix) <https://plot.ly/python/heatmaps/>`_ from tabular files. The input data contains the original/true class labels (last column) and the predicted data contains the predicted class labels (last column). The true and predicted class labels are plotted against each other. The diagonal of this heatmap shows the correctly predicted data. The plot is buried in a html file which
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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81 provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on.
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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82
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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83
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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84 ]]>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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85 </help>
c7e10084225b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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86 </tool>