Mercurial > repos > iuc > scanpy_filter
comparison filter.xml @ 11:2d02d9702d3a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
author | iuc |
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date | Wed, 08 Nov 2023 14:44:39 +0000 |
parents | b409c2486353 |
children | a03ff8633507 |
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10:b409c2486353 | 11:2d02d9702d3a |
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1 <tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@"> | 1 <tool id="scanpy_filter" name="Filter" version="@galaxy_version@" profile="@profile@"> |
2 <description>with scanpy</description> | 2 <description>with scanpy</description> |
3 <expand macro="bio_tools"/> | |
4 <macros> | 3 <macros> |
5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
6 </macros> | 5 </macros> |
6 <expand macro="bio_tools"/> | |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
10 @CMD@ | 10 @CMD@ |
11 ]]></command> | 11 ]]></command> |
50 #end if | 50 #end if |
51 #if str($method.groupby) != '' | 51 #if str($method.groupby) != '' |
52 groupby='$method.groupby', | 52 groupby='$method.groupby', |
53 #end if | 53 #end if |
54 use_raw=$method.use_raw, | 54 use_raw=$method.use_raw, |
55 log=$method.log, | |
56 key_added='$method.key_added', | 55 key_added='$method.key_added', |
57 min_in_group_fraction=$method.min_in_group_fraction, | 56 min_in_group_fraction=$method.min_in_group_fraction, |
58 max_out_group_fraction=$method.max_out_group_fraction, | 57 max_out_group_fraction=$method.max_out_group_fraction, |
59 min_fold_change=$method.min_fold_change) | 58 min_fold_change=$method.min_fold_change) |
60 | 59 |
171 </param> | 170 </param> |
172 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider"> | 171 <param argument="groupby" type="text" optional="true" label="The key of the observations grouping to consider"> |
173 <expand macro="sanitize_query" /> | 172 <expand macro="sanitize_query" /> |
174 </param> | 173 </param> |
175 <expand macro="param_use_raw"/> | 174 <expand macro="param_use_raw"/> |
176 <expand macro="param_log"/> | |
177 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values"> | 175 <param argument="key_added" type="text" value="rank_genes_groups_filtered" label="Key that will contain new values"> |
178 <expand macro="sanitize_query" /> | 176 <expand macro="sanitize_query" /> |
179 </param> | 177 </param> |
180 <param argument="min_in_group_fraction" type="float" min="0" max="1" value="0.25" label="Minimum fraction of genes expressing the gene within the categories"/> | 178 <param argument="min_in_group_fraction" type="float" min="0" max="1" value="0.25" label="Minimum fraction of genes expressing the gene within the categories"/> |
181 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/> | 179 <param argument="max_out_group_fraction" type="float" min="0" max="1" value="0.5" label="Maximum fraction of genes expressing the gene outside the categories"/> |
226 </inputs> | 224 </inputs> |
227 <outputs> | 225 <outputs> |
228 <expand macro="anndata_outputs"/> | 226 <expand macro="anndata_outputs"/> |
229 </outputs> | 227 </outputs> |
230 <tests> | 228 <tests> |
231 <test> | 229 <test expect_num_outputs="2"> |
232 <!-- test 0 --> | 230 <!-- test 1 --> |
233 <param name="adata" value="krumsiek11.h5ad" /> | 231 <param name="adata" value="krumsiek11.h5ad" /> |
234 <conditional name="method"> | 232 <conditional name="method"> |
235 <param name="method" value="pp.filter_cells"/> | 233 <param name="method" value="pp.filter_cells"/> |
236 <conditional name="filter"> | 234 <conditional name="filter"> |
237 <param name="filter" value="min_counts"/> | 235 <param name="filter" value="min_counts"/> |
250 <has_text_matching expression="min_counts=3"/> | 248 <has_text_matching expression="min_counts=3"/> |
251 </assert_contents> | 249 </assert_contents> |
252 </output> | 250 </output> |
253 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> | 251 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> |
254 </test> | 252 </test> |
255 <test> | 253 <test expect_num_outputs="2"> |
256 <!-- test 1 --> | 254 <!-- test 2 --> |
257 <param name="adata" value="krumsiek11.h5ad" /> | 255 <param name="adata" value="krumsiek11.h5ad" /> |
258 <conditional name="method"> | 256 <conditional name="method"> |
259 <param name="method" value="pp.filter_cells"/> | 257 <param name="method" value="pp.filter_cells"/> |
260 <conditional name="filter"> | 258 <conditional name="filter"> |
261 <param name="filter" value="max_genes"/> | 259 <param name="filter" value="max_genes"/> |
272 <has_text_matching expression="max_genes=100"/> | 270 <has_text_matching expression="max_genes=100"/> |
273 </assert_contents> | 271 </assert_contents> |
274 </output> | 272 </output> |
275 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/> | 273 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/> |
276 </test> | 274 </test> |
277 <test> | 275 <test expect_num_outputs="2"> |
278 <!-- test 2 --> | 276 <!-- test 3 --> |
279 <param name="adata" value="krumsiek11.h5ad" /> | 277 <param name="adata" value="krumsiek11.h5ad" /> |
280 <conditional name="method"> | 278 <conditional name="method"> |
281 <param name="method" value="pp.filter_genes"/> | 279 <param name="method" value="pp.filter_genes"/> |
282 <conditional name="filter"> | 280 <conditional name="filter"> |
283 <param name="filter" value="min_counts"/> | 281 <param name="filter" value="min_counts"/> |
293 <has_text_matching expression="min_counts=3"/> | 291 <has_text_matching expression="min_counts=3"/> |
294 </assert_contents> | 292 </assert_contents> |
295 </output> | 293 </output> |
296 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> | 294 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> |
297 </test> | 295 </test> |
298 <!-- <test> --> | 296 |
299 <!-- <!-\- test 3 -\-> --> | 297 <!-- test 4 --> |
300 <!-- <!-\- Input dataset appears to be missing rank_genes_groups key... -\-> --> | 298 <!-- Fails to write to anndata after tl.filter_rank_genes_groups |
301 <!-- <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> --> | 299 Issue has been reported here: https://github.com/scverse/anndata/issues/726 |
302 <!-- <conditional name="method"> --> | 300 The current fix is: del adata.uns['rank_genes_groups_filtered'] --> |
303 <!-- <param name="method" value="tl.filter_rank_genes_groups"/> --> | 301 <!--<test expect_num_outputs="2"> |
304 <!-- <param name="key" value="rank_genes_groups"/> --> | 302 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> |
305 <!-- <param name="use_raw" value="False"/> --> | 303 <conditional name="method"> |
306 <!-- <param name="log" value="False"/> --> | 304 <param name="method" value="tl.filter_rank_genes_groups"/> |
307 <!-- <param name="key_added" value="rank_genes_groups_filtered"/> --> | 305 <param name="key" value="rank_genes_groups"/> |
308 <!-- <param name="min_in_group_fraction" value="0.25"/> --> | 306 <param name="use_raw" value="False"/> |
309 <!-- <param name="max_out_group_fraction" value="0.5"/> --> | 307 <param name="key_added" value="rank_genes_groups_filtered"/> |
310 <!-- <param name="min_fold_change" value="3"/> --> | 308 <param name="min_in_group_fraction" value="0.25"/> |
311 <!-- </conditional> --> | 309 <param name="max_out_group_fraction" value="0.5"/> |
312 <!-- <output name="hidden_output"> --> | 310 <param name="min_fold_change" value="3"/> |
313 <!-- <assert_contents> --> | 311 </conditional> |
314 <!-- <has_text_matching expression="tl.filter_rank_genes_groups"/> --> | 312 <section name="advanced_common"> |
315 <!-- <has_text_matching expression="key='rank_genes_groups'"/> --> | 313 <param name="show_log" value="true" /> |
316 <!-- <has_text_matching expression="use_raw=False"/> --> | 314 </section> |
317 <!-- <has_text_matching expression="log=False"/> --> | 315 <output name="hidden_output"> |
318 <!-- <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> --> | 316 <assert_contents> |
319 <!-- <has_text_matching expression="min_in_group_fraction=0.25"/> --> | 317 <has_text_matching expression="tl.filter_rank_genes_groups"/> |
320 <!-- <has_text_matching expression="max_out_group_fraction=0.5"/> --> | 318 <has_text_matching expression="key='rank_genes_groups'"/> |
321 <!-- <has_text_matching expression="min_fold_change=3"/> --> | 319 <has_text_matching expression="use_raw=False"/> |
322 <!-- </assert_contents> --> | 320 <has_text_matching expression="log=False"/> |
323 <!-- </output> --> | 321 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> |
324 <!-- <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> --> | 322 <has_text_matching expression="min_in_group_fraction=0.25"/> |
325 <!-- </test> --> | 323 <has_text_matching expression="max_out_group_fraction=0.5"/> |
326 <test> | 324 <has_text_matching expression="min_fold_change=3"/> |
327 <!-- test 4 --> | 325 </assert_contents> |
326 </output> | |
327 <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> | |
328 </test>--> | |
329 <test expect_num_outputs="2"> | |
330 <!-- test 5 --> | |
328 <param name="adata" value="blobs.h5ad"/> | 331 <param name="adata" value="blobs.h5ad"/> |
329 <conditional name="method"> | 332 <conditional name="method"> |
330 <param name="method" value="pp.highly_variable_genes"/> | 333 <param name="method" value="pp.highly_variable_genes"/> |
331 <conditional name="flavor"> | 334 <conditional name="flavor"> |
332 <param name="flavor" value="seurat"/> | 335 <param name="flavor" value="seurat"/> |
351 <has_text_matching expression="subset=False"/> | 354 <has_text_matching expression="subset=False"/> |
352 </assert_contents> | 355 </assert_contents> |
353 </output> | 356 </output> |
354 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/> | 357 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.2"/> |
355 </test> | 358 </test> |
356 <test> | 359 <test expect_num_outputs="2"> |
357 <!-- test 5 --> | 360 <!-- test 6 --> |
358 <param name="adata" value="krumsiek11.h5ad" /> | 361 <param name="adata" value="krumsiek11.h5ad" /> |
359 <conditional name="method"> | 362 <conditional name="method"> |
360 <param name="method" value="pp.highly_variable_genes"/> | 363 <param name="method" value="pp.highly_variable_genes"/> |
361 <conditional name="flavor"> | 364 <conditional name="flavor"> |
362 <param name="flavor" value="cell_ranger"/> | 365 <param name="flavor" value="cell_ranger"/> |
377 <has_text_matching expression="subset=True"/> | 380 <has_text_matching expression="subset=True"/> |
378 </assert_contents> | 381 </assert_contents> |
379 </output> | 382 </output> |
380 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/> | 383 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size" delta="100000" delta_frac="0.9"/> |
381 </test> | 384 </test> |
382 <test> | 385 <test expect_num_outputs="2"> |
383 <!-- test 6 --> | 386 <!-- test 7 --> |
384 <param name="adata" value="krumsiek11.h5ad" /> | 387 <param name="adata" value="krumsiek11.h5ad" /> |
385 <conditional name="method"> | 388 <conditional name="method"> |
386 <param name="method" value="pp.subsample"/> | 389 <param name="method" value="pp.subsample"/> |
387 <conditional name="type"> | 390 <conditional name="type"> |
388 <param name="type" value="fraction" /> | 391 <param name="type" value="fraction" /> |
400 <has_text_matching expression="random_state=0"/> | 403 <has_text_matching expression="random_state=0"/> |
401 </assert_contents> | 404 </assert_contents> |
402 </output> | 405 </output> |
403 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/> | 406 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/> |
404 </test> | 407 </test> |
405 <test> | 408 <test expect_num_outputs="2"> |
406 <!-- test 7 --> | 409 <!-- test 8 --> |
407 <param name="adata" value="krumsiek11.h5ad" /> | 410 <param name="adata" value="krumsiek11.h5ad" /> |
408 <conditional name="method"> | 411 <conditional name="method"> |
409 <param name="method" value="pp.subsample"/> | 412 <param name="method" value="pp.subsample"/> |
410 <conditional name="type"> | 413 <conditional name="type"> |
411 <param name="type" value="n_obs" /> | 414 <param name="type" value="n_obs" /> |
423 <has_text_matching expression="random_state=0"/> | 426 <has_text_matching expression="random_state=0"/> |
424 </assert_contents> | 427 </assert_contents> |
425 </output> | 428 </output> |
426 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/> | 429 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/> |
427 </test> | 430 </test> |
428 <test> | 431 <test expect_num_outputs="2"> |
429 <!-- test 8 --> | 432 <!-- test 9 --> |
430 <param name="adata" value="random-randint.h5ad" /> | 433 <param name="adata" value="random-randint.h5ad" /> |
431 <conditional name="method"> | 434 <conditional name="method"> |
432 <param name="method" value="pp.downsample_counts"/> | 435 <param name="method" value="pp.downsample_counts"/> |
433 <param name="total_counts" value="20000"/> | 436 <param name="total_counts" value="20000"/> |
434 <param name="random_state" value="0"/> | 437 <param name="random_state" value="0"/> |
459 | 462 |
460 Only provide one of the optional parameters `min_counts`, `min_genes`, | 463 Only provide one of the optional parameters `min_counts`, `min_genes`, |
461 `max_counts`, `max_genes` per call. | 464 `max_counts`, `max_genes` per call. |
462 | 465 |
463 More details on the `scanpy documentation | 466 More details on the `scanpy documentation |
464 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_cells.html>`__ | 467 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_cells.html>`__ |
465 | 468 |
466 | 469 |
467 Filter genes based on number of cells or counts (`pp.filter_genes`) | 470 Filter genes based on number of cells or counts (`pp.filter_genes`) |
468 =================================================================== | 471 =================================================================== |
469 | 472 |
473 | 476 |
474 Only provide one of the optional parameters `min_counts`, `min_cells`, | 477 Only provide one of the optional parameters `min_counts`, `min_cells`, |
475 `max_counts`, `max_cells` per call. | 478 `max_counts`, `max_cells` per call. |
476 | 479 |
477 More details on the `scanpy documentation | 480 More details on the `scanpy documentation |
478 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_genes.html>`__ | 481 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_genes.html>`__ |
479 | 482 |
480 | 483 |
481 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) | 484 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) |
482 ========================================================================================================================================================== | 485 ========================================================================================================================================================== |
483 | 486 |
484 More details on the `scanpy documentation | 487 More details on the `scanpy documentation |
485 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.filter_rank_genes_groups.html>`__ | 488 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ |
486 | 489 |
487 | 490 |
488 Annotate highly variable genes (`pp.highly_variable_genes`) | 491 Annotate highly variable genes (`pp.highly_variable_genes`) |
489 =========================================================== | 492 =========================================================== |
490 | 493 |
495 | 498 |
496 Subsample to a fraction of the number of observations (`pp.subsample`) | 499 Subsample to a fraction of the number of observations (`pp.subsample`) |
497 ====================================================================== | 500 ====================================================================== |
498 | 501 |
499 More details on the `scanpy documentation | 502 More details on the `scanpy documentation |
500 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.subsample.html>`__ | 503 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.subsample.html>`__ |
501 | 504 |
502 Downsample counts (`pp.downsample_counts`) | 505 Downsample counts (`pp.downsample_counts`) |
503 ========================================== | 506 ========================================== |
504 | 507 |
505 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This | 508 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This |
506 has been implemented by M. D. Luecken. | 509 has been implemented by M. D. Luecken. |
507 | 510 |
508 More details on the `scanpy documentation | 511 More details on the `scanpy documentation |
509 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.downsample_counts.html>`__ | 512 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.downsample_counts.html>`__ |
510 | 513 |
511 | 514 |
512 ]]></help> | 515 ]]></help> |
513 <expand macro="citations"/> | 516 <expand macro="citations"/> |
514 </tool> | 517 </tool> |