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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit 271a4454eea5902e29da4b8dfa7b9124fefac6bc
author bgruening
date Tue, 07 May 2024 14:11:16 +0000
parents 62e3a4e8c54c
children f234e2e59d76
comparison
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2:62e3a4e8c54c 3:1c5dcef5ce0f
1 <tool id="plotly_ml_performance_plots" name="Plot confusion matrix, precision, recall and ROC and AUC curves" version="0.2"> 1 <tool id="plotly_ml_performance_plots" name="Plot confusion matrix, precision, recall and ROC and AUC curves" version="0.3" profile="22.05">
2 <description>of tabular data</description> 2 <description>of tabular data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.25.3">pandas</requirement> 4 <requirement type="package" version="0.10.0">galaxy-ml</requirement>
5 <requirement type="package" version="4.3.0">plotly</requirement>
6 <requirement type="package" version="0.21.3">scikit-learn</requirement>
7 <requirement type="package" version="1.4.1">scipy</requirement>
8 </requirements> 5 </requirements>
9 <version_command>echo $version</version_command> 6 <version_command>echo $version</version_command>
10 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
11 python '$__tool_directory__/plot_ml_performance.py' 8 python '$__tool_directory__/plot_ml_performance.py'
12 -i '$infile_input' 9 -i '$infile_input'
15 ]]> 12 ]]>
16 </command> 13 </command>
17 <inputs> 14 <inputs>
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."/> 15 <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."/>
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."/> 16 <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."/>
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."/> 17 <param name="infile_trained_model" type="data" format="h5mlm" label="Select trained model :" help="This file is a final model trained on training data."/>
21 </inputs> 18 </inputs>
22 19
23 <outputs> 20 <outputs>
24 <data name="output_confusion" format="html" from_work_dir="output_confusion.html" label="Confusion matrix of tabular data on ${on_string}"/> 21 <data name="output_confusion" format="html" from_work_dir="output_confusion.html" label="Confusion matrix of tabular data on ${on_string}"/>
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}"/> 22 <data name="output_prf" format="html" from_work_dir="output_prf.html" label="Precision, recall and f-score of tabular data on ${on_string}"/>
28 25
29 <tests> 26 <tests>
30 <test> 27 <test>
31 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 28 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
32 <param name="infile_output" value="binary_prediction_sgd.tabular" ftype="tabular"/> 29 <param name="infile_output" value="binary_prediction_sgd.tabular" ftype="tabular"/>
33 <param name="infile_trained_model" value="model_binary_sgd.zip" ftype="zip"/> 30 <param name="infile_trained_model" value="model_binary_sgd.h5mlm" ftype="h5mlm"/>
34 <output name="output_confusion" file="cnf_binary_sgd.html" compare="sim_size"/> 31 <output name="output_confusion">
35 <output name="output_prf" file="prf_binary_sgd.html" compare="sim_size"/> 32 <assert_contents>
36 <output name="output_roc" file="roc_auc_binary_sgd.html" compare="sim_size"/> 33 <has_size value="3486809" delta="10000" />
34 <has_text text="html" />
35 </assert_contents>
36 </output>
37 <output name="output_prf">
38 <assert_contents>
39 <has_size value="3486974" delta="10000" />
40 <has_text text="html" />
41 </assert_contents>
42 </output>
37 </test> 43 </test>
38
39 <test> 44 <test>
40 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 45 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
41 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/> 46 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/>
42 <param name="infile_trained_model" value="model_binary_linearsvm.zip" ftype="zip"/> 47 <param name="infile_trained_model" value="model_binary_linearsvm.h5mlm" ftype="h5mlm"/>
43 <output name="output_confusion" file="cnf_binary_linearsvm.html" compare="sim_size"/> 48 <output name="output_confusion">
44 <output name="output_prf" file="prf_binary_linearsvm.html" compare="sim_size"/> 49 <assert_contents>
45 <output name="output_roc" file="roc_auc_binary_linearsvm.html" compare="sim_size"/> 50 <has_size value="3486810" delta="10000" />
51 <has_text text="html" />
52 </assert_contents>
53 </output>
54 <output name="output_prf">
55 <assert_contents>
56 <has_size value="3486973" delta="10000" />
57 <has_text text="html" />
58 </assert_contents>
59 </output>
60 <output name="output_roc">
61 <assert_contents>
62 <has_size value="3497518" delta="10000" />
63 <has_text text="html" />
64 </assert_contents>
65 </output>
46 </test> 66 </test>
47
48 <test> 67 <test>
49 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 68 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
50 <param name="infile_output" value="prediction_binary_rfc.tabular" ftype="tabular"/> 69 <param name="infile_output" value="prediction_binary_rfc.tabular" ftype="tabular"/>
51 <param name="infile_trained_model" value="model_binary_rfc.zip" ftype="zip"/> 70 <param name="infile_trained_model" value="model_binary_rfc.h5mlm" ftype="h5mlm"/>
52 <output name="output_confusion" file="cnf_binary_rfc.html" compare="sim_size"/> 71 <output name="output_confusion">
53 <output name="output_prf" file="prf_binary_rfc.html" compare="sim_size"/> 72 <assert_contents>
54 <output name="output_roc" file="roc_auc_binary_rfc.html" compare="sim_size"/> 73 <has_size value="3486806" delta="10000" />
74 <has_text text="html" />
75 </assert_contents>
76 </output>
77 <output name="output_prf">
78 <assert_contents>
79 <has_size value="3486883" delta="10000" />
80 <has_text text="html" />
81 </assert_contents>
82 </output>
83 <output name="output_roc">
84 <assert_contents>
85 <has_size value="3488335" delta="10000" />
86 <has_text text="html" />
87 </assert_contents>
88 </output>
55 </test> 89 </test>
56
57 <test> 90 <test>
58 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 91 <param name="infile_input" value="binary_test_label_knn.tabular" ftype="tabular"/>
59 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/> 92 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/>
60 <param name="infile_trained_model" value="model_binary_knn.zip" ftype="zip"/> 93 <param name="infile_trained_model" value="model_binary_knn.h5mlm" ftype="h5mlm"/>
61 <output name="output_confusion" file="cnf_binary_knn.html" compare="sim_size"/> 94 <output name="output_confusion">
62 <output name="output_prf" file="prf_binary_knn.html" compare="sim_size"/> 95 <assert_contents>
63 <output name="output_roc" file="roc_auc_binary_knn.html" compare="sim_size"/> 96 <has_size value="3486856" delta="10000" />
97 <has_text text="html" />
98 </assert_contents>
99 </output>
100 <output name="output_prf">
101 <assert_contents>
102 <has_size value="3486928" delta="10000" />
103 <has_text text="html" />
104 </assert_contents>
105 </output>
106 <output name="output_roc">
107 <assert_contents>
108 <has_size value="3487215" delta="10000" />
109 <has_text text="html" />
110 </assert_contents>
111 </output>
64 </test> 112 </test>
65
66 <test> 113 <test>
67 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/> 114 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/>
68 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/> 115 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/>
69 <param name="infile_trained_model" value="model_multi_lr.zip" ftype="zip"/> 116 <param name="infile_trained_model" value="model_multi_lr.h5mlm" ftype="h5mlm"/>
70 <output name="output_confusion" file="cnf_multi_lr.html" compare="sim_size"/> 117 <output name="output_confusion">
71 <output name="output_prf" file="prf_multi_lr.html" compare="sim_size"/> 118 <assert_contents>
72 <output name="output_roc" file="roc_auc_multi_lr.html" compare="sim_size"/> 119 <has_size value="3486832" delta="10000" />
73 </test> 120 <has_text text="html" />
74 121 </assert_contents>
122 </output>
123 <output name="output_prf">
124 <assert_contents>
125 <has_size value="3487035" delta="10000" />
126 <has_text text="html" />
127 </assert_contents>
128 </output>
129 <output name="output_roc">
130 <assert_contents>
131 <has_size value="3493184" delta="10000" />
132 <has_text text="html" />
133 </assert_contents>
134 </output>
135 </test>
75 </tests> 136 </tests>
76 <help><![CDATA[ 137 <help><![CDATA[
77 **What it does** 138 **What it does**
78 139
79 140
81 provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on. 142 provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on.
82 143
83 144
84 ]]> 145 ]]>
85 </help> 146 </help>
147 <citations>
148 <citation type="doi">10.1371/journal.pcbi.1009014</citation>
149 </citations>
86 </tool> 150 </tool>