Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison cluster_reduce_dimension.xml @ 6:77b91b9bdf52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:23:29 -0500
parents 6f2d2c7f77ee
children b2df381a6004
comparison
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5:6f2d2c7f77ee 6:77b91b9bdf52
274 <option value="v1.2">v1.2</option> 274 <option value="v1.2">v1.2</option>
275 <option value="v1.0">v1.0</option> 275 <option value="v1.0">v1.0</option>
276 </param> 276 </param>
277 </when> 277 </when>
278 </conditional> 278 </conditional>
279 <expand macro="inputs_common_advanced"/>
279 </inputs> 280 </inputs>
280 <outputs> 281 <outputs>
281 <expand macro="anndata_outputs"/> 282 <expand macro="anndata_outputs"/>
282 </outputs> 283 </outputs>
283 <tests> 284 <tests>
284 <test> 285 <test>
285 <!-- test 1 --> 286 <!-- test 0 -->
286 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 287 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
287 <conditional name="method"> 288 <conditional name="method">
288 <param name="method" value="tl.louvain"/> 289 <param name="method" value="tl.louvain"/>
289 <conditional name="flavor"> 290 <conditional name="flavor">
290 <param name="flavor" value="vtraag"/> 291 <param name="flavor" value="vtraag"/>
293 <param name="random_state" value="10"/> 294 <param name="random_state" value="10"/>
294 <param name="key_added" value="louvain"/> 295 <param name="key_added" value="louvain"/>
295 <param name="directed" value="true"/> 296 <param name="directed" value="true"/>
296 <param name="use_weights" value="false"/> 297 <param name="use_weights" value="false"/>
297 </conditional> 298 </conditional>
298 <assert_stdout> 299 <section name="advanced_common">
299 <has_text_matching expression="sc.tl.louvain"/> 300 <param name="show_log" value="true" />
300 <has_text_matching expression="adata=adata"/> 301 </section>
301 <has_text_matching expression="flavor = 'vtraag'"/> 302 <output name="hidden_output">
302 <has_text_matching expression="resolution=1.0"/> 303 <assert_contents>
303 <has_text_matching expression="random_state=10"/> 304 <has_text_matching expression="sc.tl.louvain"/>
304 <has_text_matching expression="key_added='louvain'"/> 305 <has_text_matching expression="adata=adata"/>
305 <has_text_matching expression="directed=True"/> 306 <has_text_matching expression="flavor = 'vtraag'"/>
306 <has_text_matching expression="use_weights=False"/> 307 <has_text_matching expression="resolution=1.0"/>
307 </assert_stdout> 308 <has_text_matching expression="random_state=10"/>
309 <has_text_matching expression="key_added='louvain'"/>
310 <has_text_matching expression="directed=True"/>
311 <has_text_matching expression="use_weights=False"/>
312 </assert_contents>
313 </output>
308 <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 314 <output name="anndata_out" file="tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
309 </test> 315 </test>
310 <test> 316 <test>
311 <!-- test 2 --> 317 <!-- test 1 -->
312 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 318 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
313 <conditional name="method"> 319 <conditional name="method">
314 <param name="method" value="tl.leiden"/> 320 <param name="method" value="tl.leiden"/>
315 <param name="random_state" value="1"/> 321 <param name="random_state" value="1"/>
316 <param name="random_state" value="10"/> 322 <param name="random_state" value="10"/>
317 <param name="key_added" value="leiden"/> 323 <param name="key_added" value="leiden"/>
318 <param name="use_weights" value="false"/> 324 <param name="use_weights" value="false"/>
319 <param name="n_iterations" value="-1"/> 325 <param name="n_iterations" value="-1"/>
320 </conditional> 326 </conditional>
321 <assert_stdout> 327 <section name="advanced_common">
322 <has_text_matching expression="sc.tl.leiden"/> 328 <param name="show_log" value="true" />
323 <has_text_matching expression="resolution=1"/> 329 </section>
324 <has_text_matching expression="random_state=10"/> 330 <output name="hidden_output">
325 <has_text_matching expression="key_added='leiden'"/> 331 <assert_contents>
326 <has_text_matching expression="use_weights=False"/> 332 <has_text_matching expression="sc.tl.leiden"/>
327 <has_text_matching expression="n_iterations=-1"/> 333 <has_text_matching expression="resolution=1"/>
328 </assert_stdout> 334 <has_text_matching expression="random_state=10"/>
335 <has_text_matching expression="key_added='leiden'"/>
336 <has_text_matching expression="use_weights=False"/>
337 <has_text_matching expression="n_iterations=-1"/>
338 </assert_contents>
339 </output>
329 <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 340 <output name="anndata_out" file="tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
330 </test> 341 </test>
331 <test> 342 <test>
332 <!-- test 2 --> 343 <!-- test 1 -->
333 <param name="adata" value="krumsiek11.h5ad" /> 344 <param name="adata" value="krumsiek11.h5ad" />
334 <conditional name="method"> 345 <conditional name="method">
335 <param name="method" value="pp.pca"/> 346 <param name="method" value="pp.pca"/>
336 <param name="n_comps" value="50"/> 347 <param name="n_comps" value="50"/>
337 <param name="dtype" value="float32"/> 348 <param name="dtype" value="float32"/>
341 <param name="svd_solver" value="auto"/> 352 <param name="svd_solver" value="auto"/>
342 <param name="random_state" value="0"/> 353 <param name="random_state" value="0"/>
343 </conditional> 354 </conditional>
344 <param name="use_highly_variable" value="false"/> 355 <param name="use_highly_variable" value="false"/>
345 </conditional> 356 </conditional>
346 <assert_stdout> 357 <section name="advanced_common">
347 <has_text_matching expression="sc.pp.pca"/> 358 <param name="show_log" value="true" />
348 <has_text_matching expression="n_comps=50"/> 359 </section>
349 <has_text_matching expression="dtype='float32'"/> 360 <output name="hidden_output">
350 <has_text_matching expression="copy=False"/> 361 <assert_contents>
351 <has_text_matching expression="chunked=False"/> 362 <has_text_matching expression="sc.pp.pca"/>
352 <has_text_matching expression="zero_center=True"/> 363 <has_text_matching expression="n_comps=50"/>
353 <has_text_matching expression="svd_solver='auto'"/> 364 <has_text_matching expression="dtype='float32'"/>
354 <has_text_matching expression="random_state=0"/> 365 <has_text_matching expression="copy=False"/>
355 <has_text_matching expression="use_highly_variable=False"/> 366 <has_text_matching expression="chunked=False"/>
356 </assert_stdout> 367 <has_text_matching expression="zero_center=True"/>
368 <has_text_matching expression="svd_solver='auto'"/>
369 <has_text_matching expression="random_state=0"/>
370 <has_text_matching expression="use_highly_variable=False"/>
371 </assert_contents>
372 </output>
357 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 373 <output name="anndata_out" file="pp.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
358 </test> 374 </test>
359 <!--<test> 375 <!--<test>
360 < test 3 > 376 < test 3 >
361 <param name="adata" value="krumsiek11.h5ad" /> 377 <param name="adata" value="krumsiek11.h5ad" />
381 </assert_stdout> 397 </assert_stdout>
382 <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/> 398 <output name="anndata_out" file="pp.pca.krumsiek11_chunk.h5ad" ftype="h5ad" compare="sim_size"/>
383 </test> 399 </test>
384 --> 400 -->
385 <test> 401 <test>
386 <!-- test 3 --> 402 <!-- test 2 -->
387 <param name="adata" value="krumsiek11.h5ad" /> 403 <param name="adata" value="krumsiek11.h5ad" />
388 <conditional name="method"> 404 <conditional name="method">
389 <param name="method" value="tl.pca"/> 405 <param name="method" value="tl.pca"/>
390 <param name="n_comps" value="50"/> 406 <param name="n_comps" value="50"/>
391 <param name="dtype" value="float32"/> 407 <param name="dtype" value="float32"/>
395 <param name="svd_solver" value="auto"/> 411 <param name="svd_solver" value="auto"/>
396 <param name="random_state" value="0"/> 412 <param name="random_state" value="0"/>
397 </conditional> 413 </conditional>
398 <param name="use_highly_variable" value="false"/> 414 <param name="use_highly_variable" value="false"/>
399 </conditional> 415 </conditional>
400 <assert_stdout> 416 <section name="advanced_common">
401 <has_text_matching expression="sc.tl.pca"/> 417 <param name="show_log" value="true" />
402 <has_text_matching expression="n_comps=50"/> 418 </section>
403 <has_text_matching expression="dtype='float32'"/> 419 <output name="hidden_output">
404 <has_text_matching expression="copy=False"/> 420 <assert_contents>
405 <has_text_matching expression="chunked=False"/> 421 <has_text_matching expression="sc.tl.pca"/>
406 <has_text_matching expression="zero_center=True"/> 422 <has_text_matching expression="n_comps=50"/>
407 <has_text_matching expression="svd_solver='auto'"/> 423 <has_text_matching expression="dtype='float32'"/>
408 <has_text_matching expression="use_highly_variable=False"/> 424 <has_text_matching expression="copy=False"/>
409 </assert_stdout> 425 <has_text_matching expression="chunked=False"/>
426 <has_text_matching expression="zero_center=True"/>
427 <has_text_matching expression="svd_solver='auto'"/>
428 <has_text_matching expression="use_highly_variable=False"/>
429 </assert_contents>
430 </output>
410 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 431 <output name="anndata_out" file="tl.pca.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
411 </test> 432 </test>
412 <test> 433 <test>
413 <!-- test 4 --> 434 <!-- test 3 -->
414 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 435 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
415 <conditional name="method"> 436 <conditional name="method">
416 <param name="method" value="tl.diffmap"/> 437 <param name="method" value="tl.diffmap"/>
417 <param name="n_comps" value="15"/> 438 <param name="n_comps" value="15"/>
418 </conditional> 439 </conditional>
419 <assert_stdout> 440 <section name="advanced_common">
420 <has_text_matching expression="sc.tl.diffmap"/> 441 <param name="show_log" value="true" />
421 <has_text_matching expression="n_comps=15"/> 442 </section>
422 </assert_stdout> 443 <output name="hidden_output">
444 <assert_contents>
445 <has_text_matching expression="sc.tl.diffmap"/>
446 <has_text_matching expression="n_comps=15"/>
447 </assert_contents>
448 </output>
423 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 449 <output name="anndata_out" file="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
424 </test> 450 </test>
425 <test> 451 <test>
426 <!-- test 5 --> 452 <!-- test 4 -->
427 <param name="adata" value="krumsiek11.h5ad" /> 453 <param name="adata" value="krumsiek11.h5ad" />
428 <conditional name="method"> 454 <conditional name="method">
429 <param name="method" value="tl.tsne"/> 455 <param name="method" value="tl.tsne"/>
430 <param name="n_pcs" value="10"/> 456 <param name="n_pcs" value="10"/>
431 <param name="perplexity" value="30"/> 457 <param name="perplexity" value="30"/>
432 <param name="early_exaggeration" value="12.0"/> 458 <param name="early_exaggeration" value="12.0"/>
433 <param name="learning_rate" value="1000"/> 459 <param name="learning_rate" value="1000"/>
434 <param name="random_state" value="0"/> 460 <param name="random_state" value="0"/>
435 <param name="use_fast_tsne" value="true"/> 461 <param name="use_fast_tsne" value="true"/>
436 </conditional> 462 </conditional>
437 <assert_stdout> 463 <section name="advanced_common">
438 <has_text_matching expression="sc.tl.tsne"/> 464 <param name="show_log" value="true" />
439 <has_text_matching expression="n_pcs=10"/> 465 </section>
440 <has_text_matching expression="perplexity=30.0"/> 466 <output name="hidden_output">
441 <has_text_matching expression="early_exaggeration=12.0"/> 467 <assert_contents>
442 <has_text_matching expression="learning_rate=1000.0"/> 468 <has_text_matching expression="sc.tl.tsne"/>
443 <has_text_matching expression="random_state=0"/> 469 <has_text_matching expression="n_pcs=10"/>
444 <has_text_matching expression="use_fast_tsne=True"/> 470 <has_text_matching expression="perplexity=30.0"/>
445 </assert_stdout> 471 <has_text_matching expression="early_exaggeration=12.0"/>
472 <has_text_matching expression="learning_rate=1000.0"/>
473 <has_text_matching expression="random_state=0"/>
474 <has_text_matching expression="use_fast_tsne=True"/>
475 </assert_contents>
476 </output>
446 <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/> 477 <output name="anndata_out" file="tl.tsne.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>
447 </test> 478 </test>
448 <test> 479 <test>
449 <!-- test 6 --> 480 <!-- test 5 -->
450 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" /> 481 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
451 <conditional name="method"> 482 <conditional name="method">
452 <param name="method" value="tl.umap"/> 483 <param name="method" value="tl.umap"/>
453 <param name="min_dist" value="0.5"/> 484 <param name="min_dist" value="0.5"/>
454 <param name="spread" value="1.0"/> 485 <param name="spread" value="1.0"/>
458 <param name="gamma" value="1.0"/> 489 <param name="gamma" value="1.0"/>
459 <param name="negative_sample_rate" value="5"/> 490 <param name="negative_sample_rate" value="5"/>
460 <param name="init_pos" value="spectral"/> 491 <param name="init_pos" value="spectral"/>
461 <param name="random_state" value="0"/> 492 <param name="random_state" value="0"/>
462 </conditional> 493 </conditional>
463 <assert_stdout> 494 <section name="advanced_common">
464 <has_text_matching expression="sc.tl.umap"/> 495 <param name="show_log" value="true" />
465 <has_text_matching expression="min_dist=0.5"/> 496 </section>
466 <has_text_matching expression="spread=1.0"/> 497 <output name="hidden_output">
467 <has_text_matching expression="n_components=2"/> 498 <assert_contents>
468 <has_text_matching expression="maxiter=2"/> 499 <has_text_matching expression="sc.tl.umap"/>
469 <has_text_matching expression="alpha=1.0"/> 500 <has_text_matching expression="min_dist=0.5"/>
470 <has_text_matching expression="gamma=1.0"/> 501 <has_text_matching expression="spread=1.0"/>
471 <has_text_matching expression="negative_sample_rate=5"/> 502 <has_text_matching expression="n_components=2"/>
472 <has_text_matching expression="init_pos='spectral'"/> 503 <has_text_matching expression="maxiter=2"/>
473 <has_text_matching expression="random_state=0"/> 504 <has_text_matching expression="alpha=1.0"/>
474 </assert_stdout> 505 <has_text_matching expression="gamma=1.0"/>
506 <has_text_matching expression="negative_sample_rate=5"/>
507 <has_text_matching expression="init_pos='spectral'"/>
508 <has_text_matching expression="random_state=0"/>
509 </assert_contents>
510 </output>
475 <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"> 511 <output name="anndata_out" file="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size">
476 <assert_contents> 512 <assert_contents>
477 <has_h5_keys keys="X, obs, obsm, uns, var" /> 513 <has_h5_keys keys="X, obs, obsm, uns, var" />
478 </assert_contents> 514 </assert_contents>
479 </output> 515 </output>
480 </test> 516 </test>
481 <test> 517 <test>
482 <!-- test 7 --> 518 <!-- test 6 -->
483 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> 519 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
484 <conditional name="method"> 520 <conditional name="method">
485 <param name="method" value="tl.draw_graph"/> 521 <param name="method" value="tl.draw_graph"/>
486 <param name="layout" value="fa"/> 522 <param name="layout" value="fa"/>
487 <param name="random_state" value="0"/> 523 <param name="random_state" value="0"/>
488 </conditional> 524 </conditional>
489 <assert_stdout> 525 <section name="advanced_common">
490 <has_text_matching expression="sc.tl.draw_graph"/> 526 <param name="show_log" value="true" />
491 <has_text_matching expression="layout='fa'"/> 527 </section>
492 <has_text_matching expression="random_state=0"/> 528 <output name="hidden_output">
493 </assert_stdout> 529 <assert_contents>
530 <has_text_matching expression="sc.tl.draw_graph"/>
531 <has_text_matching expression="layout='fa'"/>
532 <has_text_matching expression="random_state=0"/>
533 </assert_contents>
534 </output>
494 <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 535 <output name="anndata_out" file="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
495 </test> 536 </test>
496 <test> 537 <test>
497 <!-- test 8 --> 538 <!-- test 7 -->
498 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 539 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
499 <conditional name="method"> 540 <conditional name="method">
500 <param name="method" value="tl.paga"/> 541 <param name="method" value="tl.paga"/>
501 <param name="groups" value="paul15_clusters"/> 542 <param name="groups" value="paul15_clusters"/>
502 <param name="use_rna_velocity" value="False"/> 543 <param name="use_rna_velocity" value="False"/>
503 <param name="model" value="v1.2"/> 544 <param name="model" value="v1.2"/>
504 </conditional> 545 </conditional>
505 <assert_stdout> 546 <section name="advanced_common">
506 <has_text_matching expression="sc.tl.paga"/> 547 <param name="show_log" value="true" />
507 <has_text_matching expression="groups='paul15_clusters'"/> 548 </section>
508 <has_text_matching expression="use_rna_velocity=False"/> 549 <output name="hidden_output">
509 <has_text_matching expression="model='v1.2'"/> 550 <assert_contents>
510 </assert_stdout> 551 <has_text_matching expression="sc.tl.paga"/>
552 <has_text_matching expression="groups='paul15_clusters'"/>
553 <has_text_matching expression="use_rna_velocity=False"/>
554 <has_text_matching expression="model='v1.2'"/>
555 </assert_contents>
556 </output>
511 <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 557 <output name="anndata_out" file="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
512 </test> 558 </test>
513 <test> 559 <test>
514 <!-- test 9 --> 560 <!-- test 8 -->
515 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" /> 561 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />
516 <conditional name="method"> 562 <conditional name="method">
517 <param name="method" value="tl.dpt"/> 563 <param name="method" value="tl.dpt"/>
518 <param name="n_dcs" value="15"/> 564 <param name="n_dcs" value="15"/>
519 <param name="n_branchings" value="1"/> 565 <param name="n_branchings" value="1"/>
520 <param name="min_group_size" value="0.01"/> 566 <param name="min_group_size" value="0.01"/>
521 <param name="allow_kendall_tau_shift" value="True"/> 567 <param name="allow_kendall_tau_shift" value="True"/>
522 </conditional> 568 </conditional>
523 <assert_stdout> 569 <section name="advanced_common">
524 <has_text_matching expression="sc.tl.dpt"/> 570 <param name="show_log" value="true" />
525 <has_text_matching expression="n_dcs=15"/> 571 </section>
526 <has_text_matching expression="n_branchings=1"/> 572 <output name="hidden_output">
527 <has_text_matching expression="min_group_size=0.01"/> 573 <assert_contents>
528 <has_text_matching expression="allow_kendall_tau_shift=True"/> 574 <has_text_matching expression="sc.tl.dpt"/>
529 </assert_stdout> 575 <has_text_matching expression="n_dcs=15"/>
576 <has_text_matching expression="n_branchings=1"/>
577 <has_text_matching expression="min_group_size=0.01"/>
578 <has_text_matching expression="allow_kendall_tau_shift=True"/>
579 </assert_contents>
580 </output>
530 <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/> 581 <output name="anndata_out" file="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>
531 </test> 582 </test>
532 </tests> 583 </tests>
533 <help><![CDATA[ 584 <help><![CDATA[
534 Cluster cells into subgroups (`tl.louvain`) 585 Cluster cells into subgroups (`tl.louvain`)