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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots commit daa111fcd8391d451aab39110251864fd120edf0
author bgruening
date Wed, 07 Aug 2024 10:20:05 +0000
parents 2cfa4aabda3e
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2:2cfa4aabda3e 3:e73eb091612b
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="0.4" 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="png" from_work_dir="output_confusion.png" 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}"/>
26 <data name="output_roc" format="html" from_work_dir="output_roc.html" label="ROC and AUC curves of tabular data on ${on_string}"/> 23 <data name="output_roc" format="html" from_work_dir="output_roc.html" label="ROC and AUC curves of tabular data on ${on_string}"/>
27 </outputs> 24 </outputs>
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="31751" delta="1000" />
34 </assert_contents>
35 </output>
36 <output name="output_prf">
37 <assert_contents>
38 <has_size value="3486974" delta="10000" />
39 <has_text text="html" />
40 </assert_contents>
41 </output>
37 </test> 42 </test>
38
39 <test> 43 <test>
40 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 44 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
41 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/> 45 <param name="infile_output" value="prediction_binary_linearsvm.tabular" ftype="tabular"/>
42 <param name="infile_trained_model" value="model_binary_linearsvm.zip" ftype="zip"/> 46 <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"/> 47 <output name="output_confusion">
44 <output name="output_prf" file="prf_binary_linearsvm.html" compare="sim_size"/> 48 <assert_contents>
45 <output name="output_roc" file="roc_auc_binary_linearsvm.html" compare="sim_size"/> 49 <has_size value="31983" delta="1000" />
50 </assert_contents>
51 </output>
52 <output name="output_prf">
53 <assert_contents>
54 <has_size value="3486973" delta="10000" />
55 <has_text text="html" />
56 </assert_contents>
57 </output>
58 <output name="output_roc">
59 <assert_contents>
60 <has_size value="3497518" delta="10000" />
61 <has_text text="html" />
62 </assert_contents>
63 </output>
46 </test> 64 </test>
47
48 <test> 65 <test>
49 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 66 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/>
50 <param name="infile_output" value="prediction_binary_rfc.tabular" ftype="tabular"/> 67 <param name="infile_output" value="prediction_binary_rfc.tabular" ftype="tabular"/>
51 <param name="infile_trained_model" value="model_binary_rfc.zip" ftype="zip"/> 68 <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"/> 69 <output name="output_confusion">
53 <output name="output_prf" file="prf_binary_rfc.html" compare="sim_size"/> 70 <assert_contents>
54 <output name="output_roc" file="roc_auc_binary_rfc.html" compare="sim_size"/> 71 <has_size value="34096" delta="1000" />
72 </assert_contents>
73 </output>
74 <output name="output_prf">
75 <assert_contents>
76 <has_size value="3486883" delta="10000" />
77 <has_text text="html" />
78 </assert_contents>
79 </output>
80 <output name="output_roc">
81 <assert_contents>
82 <has_size value="3488335" delta="10000" />
83 <has_text text="html" />
84 </assert_contents>
85 </output>
55 </test> 86 </test>
56
57 <test> 87 <test>
58 <param name="infile_input" value="binary_test_label.tabular" ftype="tabular"/> 88 <param name="infile_input" value="binary_test_label_knn.tabular" ftype="tabular"/>
59 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/> 89 <param name="infile_output" value="prediction_binary_knn.tabular" ftype="tabular"/>
60 <param name="infile_trained_model" value="model_binary_knn.zip" ftype="zip"/> 90 <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"/> 91 <output name="output_confusion">
62 <output name="output_prf" file="prf_binary_knn.html" compare="sim_size"/> 92 <assert_contents>
63 <output name="output_roc" file="roc_auc_binary_knn.html" compare="sim_size"/> 93 <has_size value="32398" delta="1000" />
94 </assert_contents>
95 </output>
96 <output name="output_prf">
97 <assert_contents>
98 <has_size value="3486928" delta="10000" />
99 <has_text text="html" />
100 </assert_contents>
101 </output>
102 <output name="output_roc">
103 <assert_contents>
104 <has_size value="3487215" delta="10000" />
105 <has_text text="html" />
106 </assert_contents>
107 </output>
64 </test> 108 </test>
65
66 <test> 109 <test>
67 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/> 110 <param name="infile_input" value="multi_test_label.tabular" ftype="tabular"/>
68 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/> 111 <param name="infile_output" value="prediction_multi_lr.tabular" ftype="tabular"/>
69 <param name="infile_trained_model" value="model_multi_lr.zip" ftype="zip"/> 112 <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"/> 113 <output name="output_confusion">
71 <output name="output_prf" file="prf_multi_lr.html" compare="sim_size"/> 114 <assert_contents>
72 <output name="output_roc" file="roc_auc_multi_lr.html" compare="sim_size"/> 115 <has_size value="34474" delta="1000" />
73 </test> 116 </assert_contents>
74 117 </output>
118 <output name="output_prf">
119 <assert_contents>
120 <has_size value="3487035" delta="10000" />
121 <has_text text="html" />
122 </assert_contents>
123 </output>
124 <output name="output_roc">
125 <assert_contents>
126 <has_size value="3493184" delta="10000" />
127 <has_text text="html" />
128 </assert_contents>
129 </output>
130 </test>
75 </tests> 131 </tests>
76 <help><![CDATA[ 132 <help><![CDATA[
77 **What it does** 133 **What it does**
78 134
79 135
81 provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on. 137 provides rich interactive features. Image can be saved in various format, such as 'png', 'svg', 'jpeg' and so on.
82 138
83 139
84 ]]> 140 ]]>
85 </help> 141 </help>
142 <citations>
143 <citation type="doi">10.1371/journal.pcbi.1009014</citation>
144 </citations>
86 </tool> 145 </tool>