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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit bd5f722e867bcf00eba4b08a87fcce285486fe5b
author bgruening
date Tue, 18 Jun 2019 08:26:04 -0400
parents 4fac53da862f
children 62e3a4e8c54c
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4fac53da862f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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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">
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2 <description>of tabular data</description>
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3 <requirements>
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4 <requirement type="package" version="0.22.0">pandas</requirement>
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5 <requirement type="package" version="3.1.1">plotly</requirement>
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6 <requirement type="package" version="0.19.1">scikit-learn</requirement>
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7 <requirement type="package" version="1.1.0">scipy</requirement>
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8 </requirements>
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9 <version_command>echo $version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 python '$__tool_directory__/plot_ml_performance.py'
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12 -i '$infile_input'
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13 -j '$infile_output'
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14 -k '$infile_trained_model'
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15 ]]>
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16 </command>
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17 <inputs>
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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."/>
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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."/>
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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."/>
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21 </inputs>
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23 <outputs>
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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}"/>
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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}"/>
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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}"/>
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27 </outputs>
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29 <tests>
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30 <test>
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31 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
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32 <param name="infile_output" value="binary_prediction_sgd.tabular" ftype="tabular"/>
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33 <param name="infile_trained_model" value="model_binary_sgd.zip" ftype="zip"/>
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34 <output name="output_confusion" file="cnf_binary_sgd.html" compare="sim_size"/>
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35 <output name="output_prf" file="prf_binary_sgd.html" compare="sim_size"/>
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36 <output name="output_roc" file="roc_auc_binary_sgd.html" compare="sim_size"/>
4fac53da862f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
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37 </test>
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39 <test>
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40 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
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41 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/>
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42 <param name="infile_trained_model" value="model_binary_linearsvm.zip" ftype="zip"/>
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43 <output name="output_confusion" file="cnf_binary_linearsvm.html" compare="sim_size"/>
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44 <output name="output_prf" file="prf_binary_linearsvm.html" compare="sim_size"/>
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45 <output name="output_roc" file="roc_auc_binary_linearsvm.html" compare="sim_size"/>
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46 </test>
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47
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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"/>
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51 <param name="infile_trained_model" value="model_binary_rfc.zip" ftype="zip"/>
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52 <output name="output_confusion" file="cnf_binary_rfc.html" compare="sim_size"/>
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53 <output name="output_prf" file="prf_binary_rfc.html" compare="sim_size"/>
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54 <output name="output_roc" file="roc_auc_binary_rfc.html" compare="sim_size"/>
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55 </test>
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56
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57 <test>
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58 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
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59 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/>
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60 <param name="infile_trained_model" value="model_binary_knn.zip" ftype="zip"/>
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61 <output name="output_confusion" file="cnf_binary_knn.html" compare="sim_size"/>
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62 <output name="output_prf" file="prf_binary_knn.html" compare="sim_size"/>
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63 <output name="output_roc" file="roc_auc_binary_knn.html" compare="sim_size"/>
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64 </test>
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65
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66 <test>
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67 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/>
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68 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/>
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69 <param name="infile_trained_model" value="model_multi_lr.zip" ftype="zip"/>
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70 <output name="output_confusion" file="cnf_multi_lr.html" compare="sim_size"/>
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71 <output name="output_prf" file="prf_multi_lr.html" compare="sim_size"/>
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72 <output name="output_roc" file="roc_auc_multi_lr.html" compare="sim_size"/>
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73 </test>
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74
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75 </tests>
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76 <help><![CDATA[
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77 **What it does**
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78
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79
4fac53da862f 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
4fac53da862f 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.
4fac53da862f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
parents:
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82
4fac53da862f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
parents:
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83
4fac53da862f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 8496ba724e35ba551172ea975b0fed091d4bbe88
bgruening
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84 ]]>
4fac53da862f 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>
4fac53da862f 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>