Mercurial > repos > bgruening > ml_visualization_ex

comparison ml_visualization_ex.xml @ 6:222c02df5d55 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
author bgruening
date Wed, 11 Mar 2020 13:59:57 -0400
parents 6b94d76a1397
children 6cf6f27547cb
comparison
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5:c7655b5a94af 6:222c02df5d55
19 #elif $plotting_selection.plot_type == 'feature_importances' 19 #elif $plotting_selection.plot_type == 'feature_importances'
20 --estimator '$plotting_selection.infile_estimator' 20 --estimator '$plotting_selection.infile_estimator'
21 --infile1 '$plotting_selection.infile1' 21 --infile1 '$plotting_selection.infile1'
22 #elif $plotting_selection.plot_type == 'keras_plot_model' 22 #elif $plotting_selection.plot_type == 'keras_plot_model'
23 --model_config '$plotting_selection.infile_model_config' 23 --model_config '$plotting_selection.infile_model_config'
24 #elif $plotting_selection.plot_type == 'classification_confusion_matrix'
25 --true_labels '$plotting_selection.infile_true'
26 --predicted_labels '$plotting_selection.infile_predicted'
27 --plot_color '$plotting_selection.plot_color'
28 --title '$plotting_selection.title'
24 #end if 29 #end if
25 ]]> 30 ]]>
26 </command> 31 </command>
27 <configfiles> 32 <configfiles>
28 <inputs name="inputs" /> 33 <inputs name="inputs" />
34 <option value="pr_curve">2-class / multpi-label Precison Recall curve</option> 39 <option value="pr_curve">2-class / multpi-label Precison Recall curve</option>
35 <option value="roc_curve">2-class / multi-label Receiver Operating Characteristic (ROC) curve</option> 40 <option value="roc_curve">2-class / multi-label Receiver Operating Characteristic (ROC) curve</option>
36 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option> 41 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
37 <option value="feature_importances">Feature Importances plot</option> 42 <option value="feature_importances">Feature Importances plot</option>
38 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option> 43 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
44 <option value="classification_confusion_matrix">Confusion matrix for classes</option>
39 </param> 45 </param>
40 <when value="learning_curve"> 46 <when value="learning_curve">
41 <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."/> 47 <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."/>
42 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?"/> 48 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?"/>
43 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 49 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
93 </when> 99 </when>
94 <when value="keras_plot_model"> 100 <when value="keras_plot_model">
95 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model"/> 101 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model"/>
96 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 102 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
97 <param name="plot_format" type="hidden" value="png" label="The output format and library"/> 103 <param name="plot_format" type="hidden" value="png" label="The output format and library"/>
104 </when>
105
106 <when value="classification_confusion_matrix">
107 <param name="infile_true" type="data" format="tabular" label="Select dataset containing true labels"/>
108 <param name="header_true" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
109 <conditional name="column_selector_options_true">
110 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option"
111 col_name="col1" infile="infile_true"/>
112 </conditional>
113
114 <param name="infile_predicted" type="data" format="tabular" label="Select dataset containing predicted labels"/>
115 <param name="header_predicted" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
116 <param name="title" type="text" value="Confusion matrix between true and predicted labels" label="Plot title"/>
117 <param name="plot_format" type="hidden" value="png" label="The output format and library"/>
118 <param name="plot_color" type="select" label="Choose plot color">
119 <option value="Greys">Greys</option>
120 <option value="Purples">Purples</option>
121 <option value="Blues">Blues</option>
122 <option value="Greens" selected="true">Greens</option>
123 <option value="Oranges">Oranges</option>
124 <option value="Reds">Reds</option>
125 <option value="Summer">Summer</option>
126 <option value="Autumn">Autumn</option>
127 <option value="RdYlGn">RdYlGn</option>
128 <option value="Spectral">Spectral</option>
129 <option value="winter">winter</option>
130 </param>
98 </when> 131 </when>
99 </conditional> 132 </conditional>
100 </inputs> 133 </inputs>
101 <outputs> 134 <outputs>
102 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}"> 135 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
137 </test> 170 </test>
138 <test> 171 <test>
139 <param name="plot_type" value="keras_plot_model"/> 172 <param name="plot_type" value="keras_plot_model"/>
140 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json"/> 173 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json"/>
141 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000"/> 174 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000"/>
175 </test>
176 <test>
177 <param name="plot_type" value="classification_confusion_matrix"/>
178 <param name="infile_true" value="ml_confusion_true.tabular" ftype="tabular"/>
179 <param name="header_true" value="False"/>
180 <param name="selected_column_selector_option" value="all_columns"/>
181 <param name="infile_predicted" value="ml_confusion_predicted.tabular" ftype="tabular"/>
182 <param name="header_predicted" value="False"/>
183 <param name="title" value="Confusion matrix"/>
184 <param name="plot_color" value="winter" />
185 <output name="output" file="ml_confusion_viz.png" compare="sim_size"/>
186 </test>
187 <test>
188 <param name="plot_type" value="classification_confusion_matrix"/>
189 <param name="infile_true" value="true_header.tabular" ftype="tabular"/>
190 <param name="header_true" value="True"/>
191 <param name="selected_column_selector_option" value="all_columns"/>
192 <param name="infile_predicted" value="predicted_header.tabular" ftype="tabular"/>
193 <param name="header_predicted" value="True"/>
194 <param name="title" value="Confusion matrix"/>
195 <param name="plot_color" value="winter" />
196 <output name="output" file="ml_confusion_viz.png" compare="sim_size"/>
142 </test> 197 </test>
143 </tests> 198 </tests>
144 <help> 199 <help>
145 <![CDATA[ 200 <![CDATA[
146 **What it does** 201 **What it does**