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comparison ml_visualization_ex.xml @ 0:f96efab83b65 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
author bgruening
date Fri, 13 Sep 2019 12:23:39 -0400
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1 <tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@">
2 <description>includes several types of plotting for machine learning</description>
3 <macros>
4 <import>main_macros.xml</import>
5 <import>keras_macros.xml</import>
6 </macros>
7 <expand macro="python_requirements">
8 <requirement type="package" version="3.1.1">plotly</requirement>
9 <requirement type="package" version="2.40.1">graphviz</requirement>
10 <requirement type="package" version="1.4.1">pydot</requirement>
11 </expand>
12 <expand macro="macro_stdio"/>
13 <version_command>echo "@VERSION@"</version_command>
14 <command>
15 <![CDATA[
16 python '$__tool_directory__/ml_visualization_ex.py'
17 --inputs '$inputs'
18 #if $plotting_selection.plot_type in ['learning_curve', 'rfecv_gridscores']
19 --infile1 '$plotting_selection.infile1'
20 #elif $plotting_selection.plot_type in ['pr_curve', 'roc_curve']
21 --infile1 '$plotting_selection.infile1'
22 --infile2 '$plotting_selection.infile2'
23 #elif $plotting_selection.plot_type == 'feature_importances'
24 --estimator '$plotting_selection.infile_estimator'
25 --infile1 '$plotting_selection.infile1'
26 #elif $plotting_selection.plot_type == 'keras_plot_model'
27 --model_config '$plotting_selection.infile_model_config'
28 #end if
29 ]]>
30 </command>
31 <configfiles>
32 <inputs name="inputs" />
33 </configfiles>
34 <inputs>
35 <conditional name="plotting_selection">
36 <param name="plot_type" type="select" label="Select a plotting type">
37 <option value="learning_curve" selected="true">Learning curve</option>
38 <option value="pr_curve">2-class Precison Recall curve</option>
39 <option value="roc_curve">2-class Receiver Operating Characteristic (ROC) curve</option>
40 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
41 <option value="feature_importances">Feature Importances plot</option>
42 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
43 </param>
44 <when value="learning_curve">
45 <param name="infile1" type="data" format="tabular" label="Select the dataset containing values for plotting learning curve." help="This dataset should be the output of tool model_validation->learning_curve."/>
46 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?"/>
47 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
48 </when>
49 <when value="pr_curve">
50 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="No headers. Each column corresponds to one class."/>
51 <param name="infile2" type="data" format="tabular" label="Select the dataset containing predicted probabilities." help="No headers. Each column corresponds to one class."/>
52 <param name="pos_label" type="text" value="" optional="true" label="pos_label" help="The label of positive class. If not specified, it will be 1 by default."/>
53 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
54 </when>
55 <when value="roc_curve">
56 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="No headers. Each column corresponds to one class."/>
57 <param name="infile2" type="data" format="tabular" label="Select the dataset containing predicted probabilities." help="No headers. Each column corresponds to one class."/>
58 <param name="pos_label" type="text" value="" optional="true" label="pos_label" help="The label of positive class. If not specified, it will be 1 by default."/>
59 <param name="drop_intermediate" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="true" label="drop_intermediate" help="Whether to drop some suboptimal thresholds which would not appear on a plotted ROC curve."/>
60 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
61 </when>
62 <when value="rfecv_gridscores">
63 <param name="infile1" type="data" format="tabular" label="Select the dataset containing grid_scores from a fitted RFECV object." help="Headered. Single column. Could be Output from `estimator_attributes->grid_scores_`."/>
64 <param name="steps" type="text" value="" optional="true" label="Step IDs" help="List, containing hover labels for each grid_score. For example: `list(range(10)) + [15, 20]`."/>
65 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
66 </when>
67 <when value="feature_importances">
68 <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" />
69 <param name="infile1" type="data" format="tabular" label="Select the dataset containing feature names" help="Make sure the headers (first row) are feature names."/>
70 <conditional name="column_selector_options">
71 <expand macro="samples_column_selector_options" multiple="true"/>
72 </conditional>
73 <param name="threshold" type="float" value="" optional="true" min="0." label="Threshold value" help="Features with importance below the threshold value will be ignored."/>
74 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional."/>
75 </when>
76 <when value="keras_plot_model">
77 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model"/>
78 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
79 </when>
80 </conditional>
81 </inputs>
82 <outputs>
83 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
84 <change_format>
85 <when input="plotting_selection.plot_type" value="keras_plot_model" format="png"/>
86 </change_format>
87 </data>
88 </outputs>
89 <tests>
90 <test>
91 <param name="plot_type" value="roc_curve"/>
92 <param name="infile1" value="y_true.tabular" ftype="tabular"/>
93 <param name="infile2" value="y_score.tabular" ftype="tabular"/>
94 <output name="output" file="ml_vis04.html" compare="sim_size"/>
95 </test>
96 <test>
97 <param name="plot_type" value="feature_importances"/>
98 <param name="infile_estimator" value="best_estimator_.zip" ftype="zip"/>
99 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
100 <param name="selected_column_selector_option" value="all_columns"/>
101 <output name="output" file="ml_vis01.html" compare="sim_size"/>
102 </test>
103 <test>
104 <param name="plot_type" value="learning_curve"/>
105 <param name="infile1" value="mv_result03.tabular" ftype="tabular"/>
106 <output name="output" file="ml_vis02.html" compare="sim_size"/>
107 </test>
108 <test>
109 <param name="plot_type" value="pr_curve"/>
110 <param name="infile1" value="y_true.tabular" ftype="tabular"/>
111 <param name="infile2" value="y_score.tabular" ftype="tabular"/>
112 <output name="output" file="ml_vis03.html" compare="sim_size"/>
113 </test>
114 <test>
115 <param name="plot_type" value="rfecv_gridscores"/>
116 <param name="infile1" value="grid_scores_.tabular" ftype="tabular"/>
117 <output name="output" file="ml_vis05.html" compare="sim_size"/>
118 </test>
119 <test>
120 <param name="plot_type" value="keras_plot_model"/>
121 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json"/>
122 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000"/>
123 </test>
124 </tests>
125 <help>
126 <![CDATA[
127 **What it does**
128 This tool ouputs serveral machine learning visualization plots using Plotly, including 'feature_importances', 'learning curve', 'precison recall curve', 'roc_curve', and 'number of featues vs. rfecv gridscores'. This tool also ouputs configuration diagram for a deep learning model using the Keras model JSON file as input.
129
130
131 **Feature importances**
132
133 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/feature_importances.png
134 :width: 400
135 :alt: feature importances
136
137
138 **Learning curve**
139
140 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/learning_curve.png
141 :width: 400
142 :alt: learning curve
143
144
145 **Precison recall curve**
146
147 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/pr_curve.png
148 :width: 400
149 :alt: precison recall curve
150
151
152 **Receiver operating characteristic curve**
153
154 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/roc_curve.png
155 :width: 400
156 :alt: Receiver operating characteristic curve
157
158
159 **Number of featues vs. rfecv gridscores**
160
161 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/rfecv_gridscore.png
162 :width: 400
163 :alt: Number of featues vs. rfecv gridscores
164
165
166 **Deep learning model configuration**
167
168 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/deepsea.png
169 :width: 400
170 :alt: deapsea model configuration
171 ]]>
172 </help>
173 <expand macro="sklearn_citation">
174 <citation type="bibtex">
175 @online{plotly,
176 author = {Plotly Technologies Inc.},
177 title = {Collaborative data science},
178 publisher = {Plotly Technologies Inc.},
179 address = {Montreal, QC},
180 year = {2015},
181 url = {https://plot.ly}}
182 </citation>
183 </expand>
184 </tool>