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comparison flexynesis.xml @ 1:b353dad17ab7 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
author bgruening
date Mon, 14 Apr 2025 09:56:16 +0000
parents 98431bd19f18
children
comparison
equal deleted inserted replaced
0:98431bd19f18 1:b353dad17ab7
69 --input_layers $str(",".join($input_layers)) 69 --input_layers $str(",".join($input_layers))
70 --output_layers $str(",".join($output_layers)) 70 --output_layers $str(",".join($output_layers))
71 #end if 71 #end if
72 --fusion_type $fusion_type 72 --fusion_type $fusion_type
73 --hpo_iter $hpo_iter 73 --hpo_iter $hpo_iter
74 --val_size $val_size
74 --finetuning_samples $finetuning_samples 75 --finetuning_samples $finetuning_samples
75 --variance_threshold $variance_threshold 76 --variance_threshold $variance_threshold
76 --correlation_threshold $correlation_threshold 77 --correlation_threshold $correlation_threshold
77 --subsample $subsample 78 --subsample $subsample
78 --features_min $features_min 79 --features_min $features_min
82 --hpo_patience $hpo_patience 83 --hpo_patience $hpo_patience
83 $log_transform 84 $log_transform
84 $use_loss_weighting 85 $use_loss_weighting
85 $use_cv 86 $use_cv
86 $evaluate_baseline_performance 87 $evaluate_baseline_performance
88 --feature_importance_method $feature_importance_method
87 $disable_marker_finding 89 $disable_marker_finding
88 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS} 90 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
89 ]]></command> 91 ]]></command>
90 <inputs> 92 <inputs>
91 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> 93 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
108 <option value="GNN">GNN</option> 110 <option value="GNN">GNN</option>
109 <option value="MultiTripletNetwork">MultiTripletNetwork</option> 111 <option value="MultiTripletNetwork">MultiTripletNetwork</option>
110 <option value="RandomForest">RandomForest</option> 112 <option value="RandomForest">RandomForest</option>
111 <option value="SVM">SVM</option> 113 <option value="SVM">SVM</option>
112 <option value="RandomSurvivalForest">RandomSurvivalForest</option> 114 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
115 <option value="XGBoost">XGBoost</option>
113 </param> 116 </param>
114 <when value="DirectPred"/> 117 <when value="DirectPred"/>
115 <when value="GNN"> 118 <when value="GNN">
116 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use."> 119 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">
117 <option value="GC">GC</option> 120 <option value="GC">GC</option>
131 </when> 134 </when>
132 <when value="MultiTripletNetwork"/> 135 <when value="MultiTripletNetwork"/>
133 <when value="RandomForest"/> 136 <when value="RandomForest"/>
134 <when value="SVM"/> 137 <when value="SVM"/>
135 <when value="RandomSurvivalForest"/> 138 <when value="RandomSurvivalForest"/>
139 <when value="XGBoost"/>
136 </conditional> 140 </conditional>
137 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple."> 141 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
138 <sanitizer invalid_char=""> 142 <sanitizer invalid_char="">
139 <valid initial="string.printable"></valid> 143 <valid initial="string.printable"></valid>
140 </sanitizer> 144 </sanitizer>
187 </collection> 191 </collection>
188 </outputs> 192 </outputs>
189 <tests> 193 <tests>
190 <test> 194 <test>
191 <param name="non_commercial_use" value="True"/> 195 <param name="non_commercial_use" value="True"/>
192 <param name="train_clin" value="train/clin" ftype="csv"/>
193 <param name="test_clin" value="test/clin" ftype="csv"/>
194 <param name="train_omics_main" value="train/gex" ftype="csv"/>
195 <param name="test_omics_main" value="test/gex" ftype="csv"/>
196 <param name="assay_main" value="bar"/>
197 <repeat name="omics">
198 <param name="train_omics" value="train/cnv" ftype="csv"/>
199 <param name="test_omics" value="test/cnv" ftype="csv"/>
200 <param name="assay" value="foo"/>
201 </repeat>
202 <conditional name="training_type"> 196 <conditional name="training_type">
203 <param name="model" value="s_train"/> 197 <param name="model" value="s_train"/>
204 <param name="model_class" value="DirectPred"/> 198 <param name="train_clin" value="train/clin" ftype="csv"/>
199 <param name="test_clin" value="test/clin" ftype="csv"/>
200 <param name="train_omics_main" value="train/gex" ftype="csv"/>
201 <param name="test_omics_main" value="test/gex" ftype="csv"/>
202 <param name="assay_main" value="bar"/>
203 <repeat name="omics">
204 <param name="train_omics" value="train/cnv" ftype="csv"/>
205 <param name="test_omics" value="test/cnv" ftype="csv"/>
206 <param name="assay" value="foo"/>
207 </repeat>
208 <conditional name="model_class">
209 <param name="model_class" value="DirectPred"/>
210 </conditional>
205 <param name="target_variables" value="Erlotinib"/> 211 <param name="target_variables" value="Erlotinib"/>
212 <section name="advanced">
213 <param name="hpo_iter" value="1"/>
214 </section>
206 </conditional> 215 </conditional>
207 <param name="hpo_iter" value="1"/>
208 <output_collection name="results" type="list"> 216 <output_collection name="results" type="list">
209 <element name="job.embeddings_test"> 217 <element name="job.embeddings_test">
210 <assert_contents> 218 <assert_contents>
211 <has_n_lines n="50"/> 219 <has_n_lines n="50"/>
212 </assert_contents> 220 </assert_contents>
214 <element name="job.embeddings_train"> 222 <element name="job.embeddings_train">
215 <assert_contents> 223 <assert_contents>
216 <has_n_lines n="50"/> 224 <has_n_lines n="50"/>
217 </assert_contents> 225 </assert_contents>
218 </element> 226 </element>
219 <element name="job.feature_importance"> 227 <element name="job.feature_importance.GradientShap">
220 <assert_contents> 228 <assert_contents>
221 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> 229 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
222 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> 230 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
231 <has_text_matching expression="GradientShap"/>
232 </assert_contents>
233 </element>
234 <element name="job.feature_importance.IntegratedGradients">
235 <assert_contents>
236 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
237 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
238 <has_text_matching expression="IntegratedGradients"/>
223 </assert_contents> 239 </assert_contents>
224 </element> 240 </element>
225 <element name="job.feature_logs.bar"> 241 <element name="job.feature_logs.bar">
226 <assert_contents> 242 <assert_contents>
227 <has_n_lines n="25"/> 243 <has_n_lines n="25"/>
247 </element> 263 </element>
248 </output_collection> 264 </output_collection>
249 </test> 265 </test>
250 <test> 266 <test>
251 <param name="non_commercial_use" value="True"/> 267 <param name="non_commercial_use" value="True"/>
252 <param name="train_clin" value="train/clin" ftype="csv"/>
253 <param name="test_clin" value="test/clin" ftype="csv"/>
254 <param name="train_omics_main" value="train/gex" ftype="csv"/>
255 <param name="test_omics_main" value="test/gex" ftype="csv"/>
256 <param name="assay_main" value="bar"/>
257 <conditional name="training_type"> 268 <conditional name="training_type">
258 <param name="model" value="s_train"/> 269 <param name="model" value="s_train"/>
259 <param name="model_class" value="DirectPred"/> 270 <param name="train_clin" value="train/clin" ftype="csv"/>
271 <param name="test_clin" value="test/clin" ftype="csv"/>
272 <param name="train_omics_main" value="train/gex" ftype="csv"/>
273 <param name="test_omics_main" value="test/gex" ftype="csv"/>
274 <param name="assay_main" value="bar"/>
275 <conditional name="model_class">
276 <param name="model_class" value="DirectPred"/>
277 </conditional>
260 <param name="target_variables" value="Erlotinib"/> 278 <param name="target_variables" value="Erlotinib"/>
279 <section name="advanced">
280 <param name="hpo_iter" value="1"/>
281 </section>
261 </conditional> 282 </conditional>
262 <param name="hpo_iter" value="1"/>
263 <output_collection name="results" type="list"> 283 <output_collection name="results" type="list">
264 <element name="job.embeddings_test"> 284 <element name="job.embeddings_test">
265 <assert_contents> 285 <assert_contents>
266 <has_n_lines n="50"/> 286 <has_n_lines n="50"/>
267 </assert_contents> 287 </assert_contents>
269 <element name="job.embeddings_train"> 289 <element name="job.embeddings_train">
270 <assert_contents> 290 <assert_contents>
271 <has_n_lines n="50"/> 291 <has_n_lines n="50"/>
272 </assert_contents> 292 </assert_contents>
273 </element> 293 </element>
274 <element name="job.feature_importance"> 294 <element name="job.feature_importance.GradientShap">
275 <assert_contents> 295 <assert_contents>
276 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> 296 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
277 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> 297 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
298 <has_text_matching expression="GradientShap"/>
299 </assert_contents>
300 </element>
301 <element name="job.feature_importance.IntegratedGradients">
302 <assert_contents>
303 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
304 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
305 <has_text_matching expression="IntegratedGradients"/>
278 </assert_contents> 306 </assert_contents>
279 </element> 307 </element>
280 <element name="job.feature_logs.bar"> 308 <element name="job.feature_logs.bar">
281 <assert_contents> 309 <assert_contents>
282 <has_n_lines n="25"/> 310 <has_n_lines n="25"/>
297 </element> 325 </element>
298 </output_collection> 326 </output_collection>
299 </test> 327 </test>
300 <test> 328 <test>
301 <param name="non_commercial_use" value="True"/> 329 <param name="non_commercial_use" value="True"/>
302 <param name="train_clin" value="train/clin" ftype="csv"/>
303 <param name="test_clin" value="test/clin" ftype="csv"/>
304 <param name="train_omics_main" value="train/gex" ftype="csv"/>
305 <param name="test_omics_main" value="test/gex" ftype="csv"/>
306 <param name="assay_main" value="bar"/>
307 <repeat name="omics">
308 <param name="train_omics" value="train/cnv" ftype="csv"/>
309 <param name="test_omics" value="test/cnv" ftype="csv"/>
310 <param name="assay" value="foo"/>
311 </repeat>
312 <conditional name="training_type"> 330 <conditional name="training_type">
313 <param name="model" value="s_train"/> 331 <param name="model" value="s_train"/>
314 <param name="model_class" value="DirectPred"/> 332 <param name="train_clin" value="train/clin" ftype="csv"/>
333 <param name="test_clin" value="test/clin" ftype="csv"/>
334 <param name="train_omics_main" value="train/gex" ftype="csv"/>
335 <param name="test_omics_main" value="test/gex" ftype="csv"/>
336 <param name="assay_main" value="bar"/>
337 <repeat name="omics">
338 <param name="train_omics" value="train/cnv" ftype="csv"/>
339 <param name="test_omics" value="test/cnv" ftype="csv"/>
340 <param name="assay" value="foo"/>
341 </repeat>
342 <conditional name="model_class">
343 <param name="model_class" value="DirectPred"/>
344 </conditional>
315 <param name="target_variables" value="Irinotecan"/> 345 <param name="target_variables" value="Irinotecan"/>
346 <section name="advanced">
347 <param name="hpo_iter" value="1"/>
348 </section>
316 </conditional> 349 </conditional>
317 <param name="hpo_iter" value="1"/>
318 <output_collection name="results" type="list"> 350 <output_collection name="results" type="list">
319 <element name="job.embeddings_test"> 351 <element name="job.embeddings_test">
320 <assert_contents> 352 <assert_contents>
321 <has_n_lines n="50"/> 353 <has_n_lines n="50"/>
322 </assert_contents> 354 </assert_contents>
324 <element name="job.embeddings_train"> 356 <element name="job.embeddings_train">
325 <assert_contents> 357 <assert_contents>
326 <has_n_lines n="50"/> 358 <has_n_lines n="50"/>
327 </assert_contents> 359 </assert_contents>
328 </element> 360 </element>
329 <element name="job.feature_importance"> 361 <element name="job.feature_importance.GradientShap">
330 <assert_contents> 362 <assert_contents>
331 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/> 363 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
332 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/> 364 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
365 <has_text_matching expression="GradientShap"/>
366 </assert_contents>
367 </element>
368 <element name="job.feature_importance.IntegratedGradients">
369 <assert_contents>
370 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
371 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
372 <has_text_matching expression="IntegratedGradients"/>
333 </assert_contents> 373 </assert_contents>
334 </element> 374 </element>
335 <element name="job.feature_logs.bar"> 375 <element name="job.feature_logs.bar">
336 <assert_contents> 376 <assert_contents>
337 <has_n_lines n="25"/> 377 <has_n_lines n="25"/>
338 </assert_contents> 378 </assert_contents>
339 </element> 379 </element>
340 <element name="job.feature_logs.bar"> 380 <element name="job.feature_logs.omics_foo">
341 <assert_contents> 381 <assert_contents>
342 <has_n_lines n="25"/> 382 <has_n_lines n="25"/>
343 </assert_contents> 383 </assert_contents>
344 </element> 384 </element>
345 <element name="job.predicted_labels"> 385 <element name="job.predicted_labels">
357 </element> 397 </element>
358 </output_collection> 398 </output_collection>
359 </test> 399 </test>
360 <test> 400 <test>
361 <param name="non_commercial_use" value="True"/> 401 <param name="non_commercial_use" value="True"/>
362 <param name="train_clin" value="train/clin" ftype="csv"/>
363 <param name="test_clin" value="test/clin" ftype="csv"/>
364 <param name="train_omics_main" value="train/gex" ftype="csv"/>
365 <param name="test_omics_main" value="test/gex" ftype="csv"/>
366 <param name="assay_main" value="bar"/>
367 <repeat name="omics">
368 <param name="train_omics" value="train/cnv" ftype="csv"/>
369 <param name="test_omics" value="test/cnv" ftype="csv"/>
370 <param name="assay" value="foo"/>
371 </repeat>
372 <conditional name="training_type"> 402 <conditional name="training_type">
373 <param name="model" value="us_train"/> 403 <param name="model" value="us_train"/>
404 <param name="train_clin" value="train/clin" ftype="csv"/>
405 <param name="test_clin" value="test/clin" ftype="csv"/>
406 <param name="train_omics_main" value="train/gex" ftype="csv"/>
407 <param name="test_omics_main" value="test/gex" ftype="csv"/>
408 <param name="assay_main" value="bar"/>
409 <repeat name="omics">
410 <param name="train_omics" value="train/cnv" ftype="csv"/>
411 <param name="test_omics" value="test/cnv" ftype="csv"/>
412 <param name="assay" value="foo"/>
413 </repeat>
374 <param name="model_class" value="supervised_vae"/> 414 <param name="model_class" value="supervised_vae"/>
415 <section name="advanced">
416 <param name="hpo_iter" value="1"/>
417 </section>
375 </conditional> 418 </conditional>
376 <param name="hpo_iter" value="1"/>
377 <output_collection name="results" type="list"> 419 <output_collection name="results" type="list">
378 <element name="job.embeddings_test"> 420 <element name="job.embeddings_test">
379 <assert_contents> 421 <assert_contents>
380 <has_n_lines n="50"/> 422 <has_n_lines n="50"/>
381 </assert_contents> 423 </assert_contents>
397 </element> 439 </element>
398 </output_collection> 440 </output_collection>
399 </test> 441 </test>
400 <test> 442 <test>
401 <param name="non_commercial_use" value="True"/> 443 <param name="non_commercial_use" value="True"/>
402 <param name="train_clin" value="train/clin" ftype="csv"/>
403 <param name="test_clin" value="test/clin" ftype="csv"/>
404 <param name="train_omics_main" value="train/gex" ftype="csv"/>
405 <param name="test_omics_main" value="test/gex" ftype="csv"/>
406 <param name="assay_main" value="bar"/>
407 <param name="layer_main" value="input"/>
408 <repeat name="omics">
409 <param name="train_omics" value="train/cnv" ftype="csv"/>
410 <param name="test_omics" value="test/cnv" ftype="csv"/>
411 <param name="assay" value="foo"/>
412 <param name="layer" value="output"/>
413 </repeat>
414 <conditional name="training_type"> 444 <conditional name="training_type">
415 <param name="model" value="cm_train"/> 445 <param name="model" value="cm_train"/>
446 <param name="train_clin" value="train/clin" ftype="csv"/>
447 <param name="test_clin" value="test/clin" ftype="csv"/>
448 <param name="train_omics_main" value="train/gex" ftype="csv"/>
449 <param name="test_omics_main" value="test/gex" ftype="csv"/>
450 <param name="assay_main" value="bar"/>
451 <param name="layer_main" value="input"/>
452 <repeat name="omics">
453 <param name="train_omics" value="train/cnv" ftype="csv"/>
454 <param name="test_omics" value="test/cnv" ftype="csv"/>
455 <param name="assay" value="foo"/>
456 <param name="layer" value="output"/>
457 </repeat>
416 <param name="model_class" value="CrossModalPred"/> 458 <param name="model_class" value="CrossModalPred"/>
459 <section name="advanced">
460 <param name="hpo_iter" value="1"/>
461 </section>
417 </conditional> 462 </conditional>
418 <param name="hpo_iter" value="1"/>
419 <output_collection name="results" type="list"> 463 <output_collection name="results" type="list">
420 <element name="job.embeddings_test"> 464 <element name="job.embeddings_test">
421 <assert_contents> 465 <assert_contents>
422 <has_n_lines n="50"/> 466 <has_n_lines n="50"/>
423 </assert_contents> 467 </assert_contents>
449 </element> 493 </element>
450 </output_collection> 494 </output_collection>
451 </test> 495 </test>
452 <test> 496 <test>
453 <param name="non_commercial_use" value="True"/> 497 <param name="non_commercial_use" value="True"/>
454 <param name="train_clin" value="train/clin" ftype="csv"/>
455 <param name="test_clin" value="test/clin" ftype="csv"/>
456 <param name="train_omics_main" value="train/gex" ftype="csv"/>
457 <param name="test_omics_main" value="test/gex" ftype="csv"/>
458 <param name="assay_main" value="bar"/>
459 <repeat name="omics">
460 <param name="train_omics" value="train/cnv" ftype="csv"/>
461 <param name="test_omics" value="test/cnv" ftype="csv"/>
462 <param name="assay" value="foo"/>
463 </repeat>
464 <conditional name="training_type"> 498 <conditional name="training_type">
465 <param name="model" value="s_train"/> 499 <param name="model" value="s_train"/>
466 <param name="model_class" value="GNN"/> 500 <param name="train_clin" value="train/clin" ftype="csv"/>
467 <param name="gnn_conv_type" value="GC"/> 501 <param name="test_clin" value="test/clin" ftype="csv"/>
468 <param name="string_organism" value="9606"/> 502 <param name="train_omics_main" value="train/gex" ftype="csv"/>
469 <param name="string_node_name" value="gene_name"/> 503 <param name="test_omics_main" value="test/gex" ftype="csv"/>
504 <param name="assay_main" value="bar"/>
505 <repeat name="omics">
506 <param name="train_omics" value="train/cnv" ftype="csv"/>
507 <param name="test_omics" value="test/cnv" ftype="csv"/>
508 <param name="assay" value="foo"/>
509 </repeat>
510 <conditional name="model_class">
511 <param name="model_class" value="GNN"/>
512 <param name="gnn_conv_type" value="GC"/>
513 <param name="string_organism" value="9606"/>
514 <param name="string_node_name" value="gene_name"/>
515 </conditional>
470 <param name="target_variables" value="Erlotinib"/> 516 <param name="target_variables" value="Erlotinib"/>
517 <section name="advanced">
518 <param name="hpo_iter" value="1"/>
519 </section>
471 </conditional> 520 </conditional>
472 <param name="hpo_iter" value="1"/>
473 <output_collection name="results" type="list"> 521 <output_collection name="results" type="list">
474 <element name="job.embeddings_test"> 522 <element name="job.embeddings_test">
475 <assert_contents> 523 <assert_contents>
476 <has_n_lines n="50"/> 524 <has_n_lines n="50"/>
477 </assert_contents> 525 </assert_contents>
479 <element name="job.embeddings_train"> 527 <element name="job.embeddings_train">
480 <assert_contents> 528 <assert_contents>
481 <has_n_lines n="50"/> 529 <has_n_lines n="50"/>
482 </assert_contents> 530 </assert_contents>
483 </element> 531 </element>
484 <element name="job.feature_importance"> 532 <element name="job.feature_importance.GradientShap">
485 <assert_contents> 533 <assert_contents>
486 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/> 534 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
487 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/> 535 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
536 <has_text_matching expression="GradientShap"/>
537 </assert_contents>
538 </element>
539 <element name="job.feature_importance.IntegratedGradients">
540 <assert_contents>
541 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
542 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
543 <has_text_matching expression="IntegratedGradients"/>
488 </assert_contents> 544 </assert_contents>
489 </element> 545 </element>
490 <element name="job.feature_logs.bar"> 546 <element name="job.feature_logs.bar">
491 <assert_contents> 547 <assert_contents>
492 <has_n_lines n="25"/> 548 <has_n_lines n="25"/>
503 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/> 559 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
504 </assert_contents> 560 </assert_contents>
505 </element> 561 </element>
506 <element name="job.stats"> 562 <element name="job.stats">
507 <assert_contents> 563 <assert_contents>
508 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/> 564 <has_text_matching expression="GNN,Erlotinib,numerical,mse,"/>
509 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/> 565 <has_text_matching expression="GNN,Erlotinib,numerical,r2,"/>
510 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/> 566 <has_text_matching expression="GNN,Erlotinib,numerical,pearson_corr,"/>
511 </assert_contents> 567 </assert_contents>
512 </element> 568 </element>
513 </output_collection> 569 </output_collection>
514 </test> 570 </test>
515 <test> 571 <test>
516 <param name="non_commercial_use" value="True"/> 572 <param name="non_commercial_use" value="True"/>
517 <param name="train_clin" value="train/clin" ftype="csv"/>
518 <param name="test_clin" value="test/clin" ftype="csv"/>
519 <param name="train_omics_main" value="train/gex" ftype="csv"/>
520 <param name="test_omics_main" value="test/gex" ftype="csv"/>
521 <param name="assay_main" value="b ar"/>
522 <repeat name="omics">
523 <param name="train_omics" value="train/cnv" ftype="csv"/>
524 <param name="test_omics" value="test/cnv" ftype="csv"/>
525 <param name="assay" value="f oo"/>
526 </repeat>
527 <conditional name="training_type"> 573 <conditional name="training_type">
528 <param name="model" value="us_train"/> 574 <param name="model" value="us_train"/>
575 <param name="train_clin" value="train/clin" ftype="csv"/>
576 <param name="test_clin" value="test/clin" ftype="csv"/>
577 <param name="train_omics_main" value="train/gex" ftype="csv"/>
578 <param name="test_omics_main" value="test/gex" ftype="csv"/>
579 <param name="assay_main" value="b ar"/>
580 <repeat name="omics">
581 <param name="train_omics" value="train/cnv" ftype="csv"/>
582 <param name="test_omics" value="test/cnv" ftype="csv"/>
583 <param name="assay" value="f oo"/>
584 </repeat>
529 <param name="model_class" value="supervised_vae"/> 585 <param name="model_class" value="supervised_vae"/>
586 <section name="advanced">
587 <param name="hpo_iter" value="1"/>
588 </section>
530 </conditional> 589 </conditional>
531 <param name="hpo_iter" value="1"/>
532 <output_collection name="results" type="list"> 590 <output_collection name="results" type="list">
533 <element name="job.embeddings_test"> 591 <element name="job.embeddings_test">
534 <assert_contents> 592 <assert_contents>
535 <has_n_lines n="50"/> 593 <has_n_lines n="50"/>
536 </assert_contents> 594 </assert_contents>
546 </assert_contents> 604 </assert_contents>
547 </element> 605 </element>
548 <element name="job.feature_logs.omics_f_oo"> 606 <element name="job.feature_logs.omics_f_oo">
549 <assert_contents> 607 <assert_contents>
550 <has_n_lines n="25"/> 608 <has_n_lines n="25"/>
609 </assert_contents>
610 </element>
611 </output_collection>
612 </test>
613 <test>
614 <param name="non_commercial_use" value="True"/>
615 <conditional name="training_type">
616 <param name="model" value="s_train"/>
617 <param name="train_clin" value="train/clin" ftype="csv"/>
618 <param name="test_clin" value="test/clin" ftype="csv"/>
619 <param name="train_omics_main" value="train/gex" ftype="csv"/>
620 <param name="test_omics_main" value="test/gex" ftype="csv"/>
621 <param name="assay_main" value="bar"/>
622 <repeat name="omics">
623 <param name="train_omics" value="train/cnv" ftype="csv"/>
624 <param name="test_omics" value="test/cnv" ftype="csv"/>
625 <param name="assay" value="foo"/>
626 </repeat>
627 <conditional name="model_class">
628 <param name="model_class" value="XGBoost"/>
629 </conditional>
630 <param name="target_variables" value="Erlotinib"/>
631 <section name="advanced">
632 <param name="hpo_iter" value="1"/>
633 </section>
634 </conditional>
635 <output_collection name="results" type="list">
636 <element name="job.stats">
637 <assert_contents>
638 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,mse,"/>
639 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,r2,"/>
640 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,pearson_corr,"/>
641 </assert_contents>
642 </element>
643 </output_collection>
644 </test>
645 <test>
646 <param name="non_commercial_use" value="True"/>
647 <conditional name="training_type">
648 <param name="model" value="s_train"/>
649 <param name="train_clin" value="train/clin" ftype="csv"/>
650 <param name="test_clin" value="test/clin" ftype="csv"/>
651 <param name="train_omics_main" value="train/gex" ftype="csv"/>
652 <param name="test_omics_main" value="test/gex" ftype="csv"/>
653 <param name="assay_main" value="bar"/>
654 <repeat name="omics">
655 <param name="train_omics" value="train/cnv" ftype="csv"/>
656 <param name="test_omics" value="test/cnv" ftype="csv"/>
657 <param name="assay" value="foo"/>
658 </repeat>
659 <conditional name="model_class">
660 <param name="model_class" value="DirectPred"/>
661 </conditional>
662 <param name="target_variables" value="Erlotinib"/>
663 <section name="advanced">
664 <param name="hpo_iter" value="1"/>
665 <param name="feature_importance_method" value="IntegratedGradients"/>
666 <param name="val_size" value="0.2"/>
667 </section>
668 </conditional>
669 <output_collection name="results" type="list">
670 <element name="job.embeddings_test">
671 <assert_contents>
672 <has_n_lines n="50"/>
673 </assert_contents>
674 </element>
675 <element name="job.embeddings_train">
676 <assert_contents>
677 <has_n_lines n="50"/>
678 </assert_contents>
679 </element>
680 <element name="job.feature_importance.IntegratedGradients">
681 <assert_contents>
682 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
683 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
684 </assert_contents>
685 </element>
686 <element name="job.feature_logs.bar">
687 <assert_contents>
688 <has_n_lines n="25"/>
689 </assert_contents>
690 </element>
691 <element name="job.feature_logs.omics_foo">
692 <assert_contents>
693 <has_n_lines n="25"/>
694 </assert_contents>
695 </element>
696 <element name="job.predicted_labels">
697 <assert_contents>
698 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
699 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
700 </assert_contents>
701 </element>
702 <element name="job.stats">
703 <assert_contents>
704 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
705 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
706 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
551 </assert_contents> 707 </assert_contents>
552 </element> 708 </element>
553 </output_collection> 709 </output_collection>
554 </test> 710 </test>
555 </tests> 711 </tests>