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planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
author goeckslab
date Tue, 07 Jan 2025 22:44:54 +0000
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-1:000000000000 0:dceb8493730d
1 <tool id="ludwig_visualize" name="Ludwig Visualize" version="@VERSION@" profile="@PROFILE@">
2 <description>analyzes results and shows in plots</description>
3 <macros>
4 <import>ludwig_macros.xml</import>
5 </macros>
6 <expand macro="python_requirements_gpu" />
7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command>
9 <command>
10 <![CDATA[
11 #set $visualization = $visualization_selector.visualization.value
12
13 mkdir -p "./results" &&
14 python '$__tool_directory__/ludwig_visualize.py'
15 --visualization '$visualization'
16 --output_directory "./results"
17 #if 'hyperopt_stats_path' in $visualization_selector
18 --hyperopt_stats_path '${visualization_selector.hyperopt_stats_path}'
19 #end if
20 #if 'predictions' in $visualization_selector
21 #set $pdns = [x.extra_files_path + '/predictions.parquet' for x in $visualization_selector.predictions]
22 #set $predictions = "'" + "' '".join($pdns) + "'"
23 --predictions $predictions
24 #end if
25 #if 'probabilities' in $visualization_selector
26 #set $pbts = [x.extra_files_path + '/predictions.parquet' for x in $visualization_selector.probabilities]
27 #set $probabilities = "'" + "' '".join($pbts) + "'"
28 --probabilities $probabilities
29 #end if
30 #if 'training_statistics' in $visualization_selector
31 #set $ts = []
32 #for $x in $visualization_selector.training_statistics
33 #if $x.ext != 'json'
34 $ts.append($x.extra_files_path + '/training_statistics.json')
35 #else
36 $ts.append($x.file_name)
37 #end if
38 #end for
39 #set $training_statistics = "'" + "' '".join($ts) + "'"
40 --training_statistics $training_statistics
41 #end if
42 #if 'test_statistics' in $visualization_selector
43 #set $tests = []
44 #for $tx in $visualization_selector.test_statistics
45 #if $tx.ext != 'json'
46 $tests.append($tx.extra_files_path + '/test_statistics.json')
47 #else
48 $tests.append($tx.file_name)
49 #end if
50 #end for
51 #set $test_statistics = "'" + "' '".join($tests) + "'"
52 --test_statistics $test_statistics
53 #end if
54 #if 'file_format' in $visualization_selector
55 --file_format ${visualization_selector.file_format}
56 #end if
57 #if 'ground_truth_split' in $visualization_selector
58 --ground_truth_split ${visualization_selector.ground_truth_split}
59 #end if
60 #if 'output_feature_name' in $visualization_selector and $visualization_selector.output_feature_name
61 --output_feature_name '${visualization_selector.output_feature_name}'
62 #end if
63 #if 'model_names' in $visualization_selector and $visualization_selector.model_names
64 #set $mns = $visualization_selector.model_names.split(',')
65 #set $mns = [x.strip() for x in $mns]
66 #set $model_names = "'" + "' '".join($mns) + "'"
67 --model_names $model_names
68 #end if
69 #if 'threshold_output_feature_names' in $visualization_selector
70 #set $tofns = $visualization_selector.threshold_output_feature_names.split(',')
71 #set $tofns = [x.strip() for x in $tofns]
72 #set $threshold_output_feature_names = "'" + "' '".join($tofns) + "'"
73 --threshold_output_feature_names $threshold_output_feature_names
74 #end if
75 #if 'top_n_classes' in $visualization_selector and $visualization_selector.top_n_classes
76 #set $tncs = $visualization_selector.top_n_classes.split(',')
77 #set $tncs = [x.strip() for x in $tncs]
78 #set $top_n_classes = ' '.join($tncs)
79 --top_n_classes $top_n_classes
80 #end if
81 #if 'ground_truth' in $visualization_selector
82 --ground_truth '${visualization_selector.ground_truth}'
83 #end if
84 #if 'ground_truth_metadata' in $visualization_selector
85 #if $visualization_selector.ground_truth_metadata.ext == 'json'
86 --ground_truth_metadata '${visualization_selector.ground_truth_metadata}'
87 #else
88 --ground_truth_metadata '${visualization_selector.ground_truth_metadata.extra_files_path}/training_set_metadata.json'
89 #end if
90 #end if
91 #if 'split_file' in $visualization_selector
92 --split_file '${visualization_selector.split_file}'
93 #end if
94 #if 'top_k' in $visualization_selector and $visualization_selector.top_k
95 --top_k ${visualization_selector.top_k}
96 #end if
97 #if 'labels_limit' in $visualization_selector
98 --labels_limit ${visualization_selector.labels_limit}
99 #end if
100 #if 'subset' in $visualization_selector
101 --subset ${visualization_selector.subset.value}
102 #end if
103 #if 'metrics' in $visualization_selector and $visualization_selector.metrics
104 #set $mtcs = $visualization_selector.metrics.split(',')
105 #set $mtcs = [x.strip() for x in $mtcs]
106 #set $metrics = "'" + "' '".join($mtcs) + "'"
107 --metrics ${visualization_selector.metrics}
108 #end if
109 #if 'positive_label' in $visualization_selector
110 --positive_label ${visualization_selector.positive_label}
111 #end if
112 #if 'normalize' in $visualization_selector and $visualization_selector.normalize
113 --normalize
114 #end if
115 && echo "Done!"
116 ]]>
117 </command>
118 <configfiles>
119 <inputs name="inputs" />
120 </configfiles>
121 <inputs>
122 <conditional name="visualization_selector">
123 <param name="visualization" type="select" label="Type of visualization">
124 <option value="compare_performance">compare_performance</option>
125 <option value="compare_classifiers_performance_from_prob">compare_classifiers_performance_from_prob</option>
126 <option value="compare_classifiers_performance_from_pred">compare_classifiers_performance_from_pred</option>
127 <option value="compare_classifiers_performance_subset">compare_classifiers_performance_subset</option>
128 <option value="compare_classifiers_performance_changing_k">compare_classifiers_performance_changing_k</option>
129 <option value="compare_classifiers_multiclass_multimetric">compare_classifiers_multiclass_multimetric</option>
130 <option value="compare_classifiers_predictions">compare_classifiers_predictions</option>
131 <option value="compare_classifiers_predictions_distribution">compare_classifiers_predictions_distribution</option>
132 <option value="confidence_thresholding">confidence_thresholding</option>
133 <option value="confidence_thresholding_data_vs_acc">confidence_thresholding_data_vs_acc</option>
134 <option value="confidence_thresholding_data_vs_acc_subset">confidence_thresholding_data_vs_acc_subset</option>
135 <option value="confidence_thresholding_data_vs_acc_subset_per_class">confidence_thresholding_data_vs_acc_subset_per_class</option>
136 <option value="confidence_thresholding_2thresholds_2d">confidence_thresholding_2thresholds_2d</option>
137 <option value="confidence_thresholding_2thresholds_3d">confidence_thresholding_2thresholds_3d</option>
138 <option value="binary_threshold_vs_metric">binary_threshold_vs_metric</option>
139 <option value="roc_curves">roc_curves</option>
140 <option value="roc_curves_from_test_statistics">roc_curves_from_test_statistics</option>
141 <option value="calibration_1_vs_all">calibration_1_vs_all</option>
142 <option value="calibration_multiclass">calibration_multiclass</option>
143 <option value="confusion_matrix">confusion_matrix</option>
144 <option value="frequency_vs_f1">frequency_vs_f1</option>
145 <option value="learning_curves">learning_curves</option>
146 <option value="hyperopt_report" selected="true">hyperopt_report</option>
147 <option value="hyperopt_hiplot">hyperopt_hiplot</option>
148 </param>
149 <when value="compare_performance">
150 <expand macro="visualize_test_statistics" />
151 <expand macro="visualize_output_feature_name" />
152 <expand macro="visualize_model_names" />
153 <expand macro="visualize_file_format" />
154 </when>
155 <when value="compare_classifiers_performance_from_prob">
156 <expand macro="visualize_probabilities" />
157 <expand macro="visualize_ground_truth" />
158 <expand macro="visualize_ground_truth_split" />
159 <expand macro="visualize_split_file" />
160 <expand macro="visualize_ground_truth_metadata" />
161 <expand macro="visualize_output_feature_name" />
162 </when>
163 <when value="compare_classifiers_performance_from_pred">
164 <expand macro="visualize_predictions" />
165 <expand macro="visualize_ground_truth" />
166 <expand macro="visualize_ground_truth_split" />
167 <expand macro="visualize_split_file" />
168 <expand macro="visualize_ground_truth_metadata" />
169 <expand macro="visualize_output_feature_name" />
170 </when>
171 <when value="compare_classifiers_performance_subset">
172 <expand macro="visualize_probabilities" />
173 <expand macro="visualize_ground_truth" />
174 <expand macro="visualize_ground_truth_split" />
175 <expand macro="visualize_split_file" />
176 <expand macro="visualize_ground_truth_metadata" />
177 <expand macro="visualize_output_feature_name" />
178 </when>
179 <when value="compare_classifiers_performance_changing_k">
180 <expand macro="visualize_probabilities" />
181 <expand macro="visualize_ground_truth" />
182 <expand macro="visualize_ground_truth_split" />
183 <expand macro="visualize_split_file" />
184 <expand macro="visualize_ground_truth_metadata" />
185 <expand macro="visualize_output_feature_name" />
186 </when>
187 <when value="compare_classifiers_multiclass_multimetric">
188 <expand macro="visualize_test_statistics" />
189 <expand macro="visualize_ground_truth_metadata" />
190 <expand macro="visualize_output_feature_name" />
191 <expand macro="visualize_top_n_classes" />
192 <expand macro="visualize_model_names" />
193 <expand macro="visualize_file_format" />
194 </when>
195 <when value="compare_classifiers_predictions">
196 <expand macro="visualize_predictions" />
197 <expand macro="visualize_ground_truth" />
198 <expand macro="visualize_ground_truth_split" />
199 <expand macro="visualize_split_file" />
200 <expand macro="visualize_ground_truth_metadata" />
201 <expand macro="visualize_output_feature_name" />
202 </when>
203 <when value="compare_classifiers_predictions_distribution">
204 <expand macro="visualize_predictions" />
205 <expand macro="visualize_ground_truth" />
206 <expand macro="visualize_ground_truth_split" />
207 <expand macro="visualize_split_file" />
208 <expand macro="visualize_ground_truth_metadata" />
209 <expand macro="visualize_output_feature_name" />
210 </when>
211 <when value="confidence_thresholding">
212 <expand macro="visualize_probabilities" />
213 <expand macro="visualize_ground_truth" />
214 <expand macro="visualize_ground_truth_split" />
215 <expand macro="visualize_split_file" />
216 <expand macro="visualize_ground_truth_metadata" />
217 <expand macro="visualize_output_feature_name" />
218 </when>
219 <when value="confidence_thresholding_data_vs_acc">
220 <expand macro="visualize_probabilities" />
221 <expand macro="visualize_ground_truth" />
222 <expand macro="visualize_ground_truth_split" />
223 <expand macro="visualize_split_file" />
224 <expand macro="visualize_ground_truth_metadata" />
225 <expand macro="visualize_output_feature_name" />
226 </when>
227 <when value="confidence_thresholding_data_vs_acc_subset">
228 <expand macro="visualize_probabilities" />
229 <expand macro="visualize_ground_truth" />
230 <expand macro="visualize_ground_truth_split" />
231 <expand macro="visualize_split_file" />
232 <expand macro="visualize_ground_truth_metadata" />
233 <expand macro="visualize_output_feature_name" />
234 </when>
235 <when value="confidence_thresholding_data_vs_acc_subset_per_class">
236 <expand macro="visualize_probabilities" />
237 <expand macro="visualize_ground_truth" />
238 <expand macro="visualize_ground_truth_split" />
239 <expand macro="visualize_split_file" />
240 <expand macro="visualize_ground_truth_metadata" />
241 <expand macro="visualize_output_feature_name" />
242 </when>
243 <when value="confidence_thresholding_2thresholds_2d">
244 <expand macro="visualize_probabilities" />
245 <expand macro="visualize_ground_truth" />
246 <expand macro="visualize_ground_truth_split" />
247 <expand macro="visualize_split_file" />
248 <expand macro="visualize_ground_truth_metadata" />
249 <expand macro="visualize_threshold_output_feature_names" />
250 <expand macro="visualize_labels_limit" />
251 <expand macro="visualize_model_names" />
252 <expand macro="visualize_file_format" />
253 </when>
254 <when value="confidence_thresholding_2thresholds_3d">
255 <expand macro="visualize_probabilities" />
256 <expand macro="visualize_ground_truth" />
257 <expand macro="visualize_ground_truth_split" />
258 <expand macro="visualize_split_file" />
259 <expand macro="visualize_ground_truth_metadata" />
260 <expand macro="visualize_threshold_output_feature_names" />
261 <expand macro="visualize_labels_limit" />
262 <expand macro="visualize_file_format" />
263 </when>
264 <when value="binary_threshold_vs_metric">
265 <expand macro="visualize_probabilities" />
266 <expand macro="visualize_ground_truth" />
267 <expand macro="visualize_ground_truth_split" />
268 <expand macro="visualize_split_file" />
269 <expand macro="visualize_ground_truth_metadata" />
270 <expand macro="visualize_output_feature_name" />
271 <expand macro="visualize_metrics" />
272 <expand macro="visualize_positive_label" />
273 <expand macro="visualize_model_names" />
274 <expand macro="visualize_file_format" />
275 </when>
276 <when value="roc_curves">
277 <expand macro="visualize_probabilities" />
278 <expand macro="visualize_ground_truth" />
279 <expand macro="visualize_ground_truth_split" />
280 <expand macro="visualize_split_file" />
281 <expand macro="visualize_ground_truth_metadata" />
282 <expand macro="visualize_output_feature_name" />
283 <expand macro="visualize_positive_label" />
284 <expand macro="visualize_model_names" />
285 <expand macro="visualize_file_format" />
286 </when>
287 <when value="roc_curves_from_test_statistics">
288 <expand macro="visualize_test_statistics" />
289 <expand macro="visualize_output_feature_name" />
290 <expand macro="visualize_model_names" />
291 <expand macro="visualize_file_format" />
292 </when>
293 <when value="calibration_1_vs_all">
294 <expand macro="visualize_probabilities" />
295 <expand macro="visualize_ground_truth" />
296 <expand macro="visualize_ground_truth_split" />
297 <expand macro="visualize_split_file" />
298 <expand macro="visualize_ground_truth_metadata" />
299 <expand macro="visualize_output_feature_name" />
300 <expand macro="visualize_ground_truth_apply_idx" />
301 </when>
302 <when value="calibration_multiclass">
303 <expand macro="visualize_probabilities" />
304 <expand macro="visualize_ground_truth" />
305 <expand macro="visualize_ground_truth_split" />
306 <expand macro="visualize_split_file" />
307 <expand macro="visualize_ground_truth_metadata" />
308 <expand macro="visualize_output_feature_name" />
309 <expand macro="visualize_labels_limit" />
310 <expand macro="visualize_model_names" />
311 <expand macro="visualize_file_format" />
312 <expand macro="visualize_ground_truth_apply_idx" />
313 </when>
314 <when value="confusion_matrix">
315 <expand macro="visualize_test_statistics" />
316 <expand macro="visualize_ground_truth_metadata" />
317 <expand macro="visualize_output_feature_name" />
318 <expand macro="visualize_top_n_classes" />
319 <expand macro="visualize_normalize" />
320 <expand macro="visualize_model_names" />
321 <expand macro="visualize_file_format" />
322 </when>
323 <when value="frequency_vs_f1">
324 <expand macro="visualize_test_statistics" />
325 <expand macro="visualize_ground_truth_metadata" />
326 <expand macro="visualize_output_feature_name" />
327 <expand macro="visualize_top_n_classes" />
328 <expand macro="visualize_model_names" />
329 <expand macro="visualize_file_format" />
330 </when>
331 <when value="learning_curves">
332 <expand macro="visualize_training_statistics" />
333 <expand macro="visualize_output_feature_name" />
334 <expand macro="visualize_model_names" />
335 <expand macro="visualize_file_format" />
336 </when>
337 <when value="hyperopt_report">
338 <expand macro="visualize_hyperopt_stats_path" />
339 <expand macro="visualize_file_format" />
340 </when>
341 <when value="hyperopt_hiplot">
342 <expand macro="visualize_hyperopt_stats_path" />
343 </when>
344 </conditional>
345 </inputs>
346 <outputs>
347 <collection type="list" name="output" label="${tool.name} ${visualization_selector.visualization} on ${on_string}">
348 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" directory="results" />
349 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="results" />
350 </collection>
351 </outputs>
352 <tests>
353 <test>
354 <conditional name="visualization_selector">
355 <param name="visualization" value="hyperopt_report" />
356 <param name="hyperopt_stats_path" value="temperature_hyperopt_statistics.json" ftype="json" />
357 <param name="file_type" value="pdf" />
358 </conditional>
359 <output_collection name="output" type="list">
360 <element name="hyperopt_trainer.learning_rate" file="temp_hyperopt_training.learning_rate.pdf" ftype="pdf" />
361 </output_collection>
362 </test>
363 </tests>
364 <help>
365 <![CDATA[
366 **What it does**
367 This tool supports various of visualizations from Ludwig.
368
369
370 **Input**
371 Report output from ludwig train/experiment/evaluate/predict tool.
372
373
374 **Output**
375 PNG or PDF.
376
377
378 ]]>
379 </help>
380 <expand macro="macro_citations" />
381 </tool>