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comparison filter.xml @ 6:9a9944c53825 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 13:21:39 +0000
parents 6d102b066d0c
children 3984cbbf0b5a
comparison
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5:6d102b066d0c 6:9a9944c53825
213 <param argument="total_counts" type="integer" min="0" optional="true" label="Target total counts" help="If the count matrix has more than total_counts it will be downsampled to have this number."/> 213 <param argument="total_counts" type="integer" min="0" optional="true" label="Target total counts" help="If the count matrix has more than total_counts it will be downsampled to have this number."/>
214 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/> 214 <param argument="random_state" type="integer" value="0" label="Random seed to change subsampling"/>
215 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/> 215 <param argument="replace" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Sample the counts with replacement?"/>
216 </when> 216 </when>
217 </conditional> 217 </conditional>
218 <expand macro="inputs_common_advanced"/>
218 </inputs> 219 </inputs>
219 <outputs> 220 <outputs>
220 <expand macro="anndata_outputs"/> 221 <expand macro="anndata_outputs"/>
221 </outputs> 222 </outputs>
222 <tests> 223 <tests>
223 <test> 224 <test>
224 <!-- test 1 --> 225 <!-- test 0 -->
225 <param name="adata" value="krumsiek11.h5ad" /> 226 <param name="adata" value="krumsiek11.h5ad" />
226 <conditional name="method"> 227 <conditional name="method">
227 <param name="method" value="pp.filter_cells"/> 228 <param name="method" value="pp.filter_cells"/>
228 <conditional name="filter"> 229 <conditional name="filter">
229 <param name="filter" value="min_counts"/> 230 <param name="filter" value="min_counts"/>
230 <param name="min_counts" value="3"/> 231 <param name="min_counts" value="3"/>
231 </conditional> 232 </conditional>
232 </conditional> 233 </conditional>
233 <assert_stdout> 234 <assert_stdout>
234 <has_text_matching expression="sc.pp.filter_cells"/> 235 <has_text_matching expression="336 × 11"/>
235 <has_text_matching expression="min_counts=3"/>
236 </assert_stdout> 236 </assert_stdout>
237 <section name="advanced_common">
238 <param name="show_log" value="true" />
239 </section>
240 <output name="hidden_output">
241 <assert_contents>
242 <has_text_matching expression="sc.pp.filter_cells"/>
243 <has_text_matching expression="min_counts=3"/>
244 </assert_contents>
245 </output>
237 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> 246 <output name="anndata_out" file="pp.filter_cells.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
238 </test> 247 </test>
239 <test> 248 <test>
240 <!-- test 2 --> 249 <!-- test 1 -->
241 <param name="adata" value="krumsiek11.h5ad" /> 250 <param name="adata" value="krumsiek11.h5ad" />
242 <conditional name="method"> 251 <conditional name="method">
243 <param name="method" value="pp.filter_cells"/> 252 <param name="method" value="pp.filter_cells"/>
244 <conditional name="filter"> 253 <conditional name="filter">
245 <param name="filter" value="max_genes"/> 254 <param name="filter" value="max_genes"/>
246 <param name="max_genes" value="100"/> 255 <param name="max_genes" value="100"/>
247 </conditional> 256 </conditional>
248 </conditional> 257 </conditional>
249 <assert_stdout> 258 <section name="advanced_common">
250 <has_text_matching expression="sc.pp.filter_cells"/> 259 <param name="show_log" value="true" />
251 <has_text_matching expression="adata"/> 260 </section>
252 <has_text_matching expression="max_genes=100"/> 261 <output name="hidden_output">
253 </assert_stdout> 262 <assert_contents>
263 <has_text_matching expression="sc.pp.filter_cells"/>
264 <has_text_matching expression="adata"/>
265 <has_text_matching expression="max_genes=100"/>
266 </assert_contents>
267 </output>
254 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/> 268 <output name="anndata_out" file="pp.filter_cells.krumsiek11-max_genes.h5ad" ftype="h5ad" compare="sim_size"/>
255 </test> 269 </test>
256 <test> 270 <test>
257 <!-- test 3 --> 271 <!-- test 2 -->
258 <param name="adata" value="krumsiek11.h5ad" /> 272 <param name="adata" value="krumsiek11.h5ad" />
259 <conditional name="method"> 273 <conditional name="method">
260 <param name="method" value="pp.filter_genes"/> 274 <param name="method" value="pp.filter_genes"/>
261 <conditional name="filter"> 275 <conditional name="filter">
262 <param name="filter" value="min_counts"/> 276 <param name="filter" value="min_counts"/>
263 <param name="min_counts" value="3"/> 277 <param name="min_counts" value="3"/>
264 </conditional> 278 </conditional>
265 </conditional> 279 </conditional>
266 <assert_stdout> 280 <section name="advanced_common">
267 <has_text_matching expression="sc.pp.filter_genes"/> 281 <param name="show_log" value="true" />
268 <has_text_matching expression="min_counts=3"/> 282 </section>
269 </assert_stdout> 283 <output name="hidden_output">
284 <assert_contents>
285 <has_text_matching expression="sc.pp.filter_genes"/>
286 <has_text_matching expression="min_counts=3"/>
287 </assert_contents>
288 </output>
270 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/> 289 <output name="anndata_out" file="pp.filter_genes.krumsiek11-min_counts.h5ad" ftype="h5ad" compare="sim_size"/>
271 </test> 290 </test>
291 <!-- <test> -->
292 <!-- <!-\- test 3 -\-> -->
293 <!-- <!-\- Input dataset appears to be missing rank_genes_groups key... -\-> -->
294 <!-- <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" /> -->
295 <!-- <conditional name="method"> -->
296 <!-- <param name="method" value="tl.filter_rank_genes_groups"/> -->
297 <!-- <param name="key" value="rank_genes_groups"/> -->
298 <!-- <param name="use_raw" value="False"/> -->
299 <!-- <param name="log" value="False"/> -->
300 <!-- <param name="key_added" value="rank_genes_groups_filtered"/> -->
301 <!-- <param name="min_in_group_fraction" value="0.25"/> -->
302 <!-- <param name="max_out_group_fraction" value="0.5"/> -->
303 <!-- <param name="min_fold_change" value="3"/> -->
304 <!-- </conditional> -->
305 <!-- <output name="hidden_output"> -->
306 <!-- <assert_contents> -->
307 <!-- <has_text_matching expression="tl.filter_rank_genes_groups"/> -->
308 <!-- <has_text_matching expression="key='rank_genes_groups'"/> -->
309 <!-- <has_text_matching expression="use_raw=False"/> -->
310 <!-- <has_text_matching expression="log=False"/> -->
311 <!-- <has_text_matching expression="key_added='rank_genes_groups_filtered'"/> -->
312 <!-- <has_text_matching expression="min_in_group_fraction=0.25"/> -->
313 <!-- <has_text_matching expression="max_out_group_fraction=0.5"/> -->
314 <!-- <has_text_matching expression="min_fold_change=3"/> -->
315 <!-- </assert_contents> -->
316 <!-- </output> -->
317 <!-- <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/> -->
318 <!-- </test> -->
272 <test> 319 <test>
273 <!-- test 4 --> 320 <!-- test 4 -->
274 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
275 <conditional name="method">
276 <param name="method" value="tl.filter_rank_genes_groups"/>
277 <param name="key" value="rank_genes_groups"/>
278 <param name="use_raw" value="False"/>
279 <param name="log" value="False"/>
280 <param name="key_added" value="rank_genes_groups_filtered"/>
281 <param name="min_in_group_fraction" value="0.25"/>
282 <param name="max_out_group_fraction" value="0.5"/>
283 <param name="min_fold_change" value="3"/>
284 </conditional>
285 <assert_stdout>
286 <has_text_matching expression="tl.filter_rank_genes_groups"/>
287 <has_text_matching expression="key='rank_genes_groups'"/>
288 <has_text_matching expression="use_raw=False"/>
289 <has_text_matching expression="log=False"/>
290 <has_text_matching expression="key_added='rank_genes_groups_filtered'"/>
291 <has_text_matching expression="min_in_group_fraction=0.25"/>
292 <has_text_matching expression="max_out_group_fraction=0.5"/>
293 <has_text_matching expression="min_fold_change=3"/>
294 </assert_stdout>
295 <output name="anndata_out" file="pp.filter_rank_genes_groups.h5ad" ftype="h5ad" compare="sim_size"/>
296 </test>
297 <test>
298 <!-- test 5 -->
299 <param name="adata" value="blobs.h5ad"/> 321 <param name="adata" value="blobs.h5ad"/>
300 <conditional name="method"> 322 <conditional name="method">
301 <param name="method" value="pp.highly_variable_genes"/> 323 <param name="method" value="pp.highly_variable_genes"/>
302 <conditional name="flavor"> 324 <conditional name="flavor">
303 <param name="flavor" value="seurat"/> 325 <param name="flavor" value="seurat"/>
306 <param name="min_disp" value="0.5"/> 328 <param name="min_disp" value="0.5"/>
307 </conditional> 329 </conditional>
308 <param name="n_bins" value="20"/> 330 <param name="n_bins" value="20"/>
309 <param name="subset" value="false"/> 331 <param name="subset" value="false"/>
310 </conditional> 332 </conditional>
311 <assert_stdout> 333 <section name="advanced_common">
312 <has_text_matching expression="sc.pp.highly_variable_genes"/> 334 <param name="show_log" value="true" />
313 <has_text_matching expression="flavor='seurat'"/> 335 </section>
314 <has_text_matching expression="min_mean=0.0125"/> 336 <output name="hidden_output">
315 <has_text_matching expression="max_mean=3"/> 337 <assert_contents>
316 <has_text_matching expression="min_disp=0.5"/> 338 <has_text_matching expression="sc.pp.highly_variable_genes"/>
317 <has_text_matching expression="n_bins=20"/> 339 <has_text_matching expression="flavor='seurat'"/>
318 <has_text_matching expression="subset=False"/> 340 <has_text_matching expression="min_mean=0.0125"/>
319 </assert_stdout> 341 <has_text_matching expression="max_mean=3"/>
342 <has_text_matching expression="min_disp=0.5"/>
343 <has_text_matching expression="n_bins=20"/>
344 <has_text_matching expression="subset=False"/>
345 </assert_contents>
346 </output>
320 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size"/> 347 <output name="anndata_out" file="pp.highly_variable_genes.seurat.blobs.h5ad" ftype="h5ad" compare="sim_size"/>
321 </test> 348 </test>
322 <test> 349 <test>
323 <!-- test 6 --> 350 <!-- test 5 -->
324 <param name="adata" value="krumsiek11.h5ad" /> 351 <param name="adata" value="krumsiek11.h5ad" />
325 <conditional name="method"> 352 <conditional name="method">
326 <param name="method" value="pp.highly_variable_genes"/> 353 <param name="method" value="pp.highly_variable_genes"/>
327 <conditional name="flavor"> 354 <conditional name="flavor">
328 <param name="flavor" value="cell_ranger"/> 355 <param name="flavor" value="cell_ranger"/>
329 <param name="n_top_genes" value="2"/> 356 <param name="n_top_genes" value="2"/>
330 </conditional> 357 </conditional>
331 <param name="n_bins" value="20"/> 358 <param name="n_bins" value="20"/>
332 <param name="subset" value="true"/> 359 <param name="subset" value="true"/>
333 </conditional> 360 </conditional>
334 <assert_stdout> 361 <section name="advanced_common">
335 <has_text_matching expression="sc.pp.highly_variable_genes"/> 362 <param name="show_log" value="true" />
336 <has_text_matching expression="flavor='cell_ranger'"/> 363 </section>
337 <has_text_matching expression="n_top_genes=2"/> 364 <output name="hidden_output">
338 <has_text_matching expression="n_bins=20"/> 365 <assert_contents>
339 <has_text_matching expression="subset=True"/> 366 <has_text_matching expression="sc.pp.highly_variable_genes"/>
340 </assert_stdout> 367 <has_text_matching expression="flavor='cell_ranger'"/>
368 <has_text_matching expression="n_top_genes=2"/>
369 <has_text_matching expression="n_bins=20"/>
370 <has_text_matching expression="subset=True"/>
371 </assert_contents>
372 </output>
341 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/> 373 <output name="anndata_out" file="pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad" ftype="h5ad" compare="sim_size"/>
342 </test> 374 </test>
343 <test> 375 <test>
344 <!-- test 7 --> 376 <!-- test 6 -->
345 <param name="adata" value="krumsiek11.h5ad" /> 377 <param name="adata" value="krumsiek11.h5ad" />
346 <conditional name="method"> 378 <conditional name="method">
347 <param name="method" value="pp.subsample"/> 379 <param name="method" value="pp.subsample"/>
348 <conditional name="type"> 380 <conditional name="type">
349 <param name="type" value="fraction" /> 381 <param name="type" value="fraction" />
350 <param name="fraction" value="0.5"/> 382 <param name="fraction" value="0.5"/>
351 </conditional> 383 </conditional>
352 <param name="random_state" value="0"/> 384 <param name="random_state" value="0"/>
353 </conditional> 385 </conditional>
354 <assert_stdout> 386 <section name="advanced_common">
355 <has_text_matching expression="sc.pp.subsample"/> 387 <param name="show_log" value="true" />
356 <has_text_matching expression="fraction=0.5"/> 388 </section>
357 <has_text_matching expression="random_state=0"/> 389 <output name="hidden_output">
358 </assert_stdout> 390 <assert_contents>
391 <has_text_matching expression="sc.pp.subsample"/>
392 <has_text_matching expression="fraction=0.5"/>
393 <has_text_matching expression="random_state=0"/>
394 </assert_contents>
395 </output>
359 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/> 396 <output name="anndata_out" file="pp.subsample.krumsiek11_fraction.h5ad" ftype="h5ad" compare="sim_size"/>
360 </test> 397 </test>
361 <test> 398 <test>
362 <!-- test 8 --> 399 <!-- test 7 -->
363 <param name="adata" value="krumsiek11.h5ad" /> 400 <param name="adata" value="krumsiek11.h5ad" />
364 <conditional name="method"> 401 <conditional name="method">
365 <param name="method" value="pp.subsample"/> 402 <param name="method" value="pp.subsample"/>
366 <conditional name="type"> 403 <conditional name="type">
367 <param name="type" value="n_obs" /> 404 <param name="type" value="n_obs" />
368 <param name="n_obs" value="10"/> 405 <param name="n_obs" value="10"/>
369 </conditional> 406 </conditional>
370 <param name="random_state" value="0"/> 407 <param name="random_state" value="0"/>
371 </conditional> 408 </conditional>
372 <assert_stdout> 409 <section name="advanced_common">
373 <has_text_matching expression="sc.pp.subsample"/> 410 <param name="show_log" value="true" />
374 <has_text_matching expression="n_obs=10"/> 411 </section>
375 <has_text_matching expression="random_state=0"/> 412 <output name="hidden_output">
376 </assert_stdout> 413 <assert_contents>
414 <has_text_matching expression="sc.pp.subsample"/>
415 <has_text_matching expression="n_obs=10"/>
416 <has_text_matching expression="random_state=0"/>
417 </assert_contents>
418 </output>
377 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/> 419 <output name="anndata_out" file="pp.subsample.krumsiek11_n_obs.h5ad" ftype="h5ad" compare="sim_size"/>
378 </test> 420 </test>
379 <test> 421 <test>
380 <!-- test 9 --> 422 <!-- test 8 -->
381 <param name="adata" value="random-randint.h5ad" /> 423 <param name="adata" value="random-randint.h5ad" />
382 <conditional name="method"> 424 <conditional name="method">
383 <param name="method" value="pp.downsample_counts"/> 425 <param name="method" value="pp.downsample_counts"/>
384 <param name="total_counts" value="20000"/> 426 <param name="total_counts" value="20000"/>
385 <param name="random_state" value="0"/> 427 <param name="random_state" value="0"/>
386 <param name="replace" value="false"/> 428 <param name="replace" value="false"/>
387 </conditional> 429 </conditional>
388 <assert_stdout> 430 <section name="advanced_common">
389 <has_text_matching expression="sc.pp.downsample_counts"/> 431 <param name="show_log" value="true" />
390 <has_text_matching expression="total_counts=20000"/> 432 </section>
391 <has_text_matching expression="random_state=0"/> 433 <output name="hidden_output">
392 <has_text_matching expression="replace=False"/> 434 <assert_contents>
393 </assert_stdout> 435 <has_text_matching expression="sc.pp.downsample_counts"/>
436 <has_text_matching expression="total_counts=20000"/>
437 <has_text_matching expression="random_state=0"/>
438 <has_text_matching expression="replace=False"/>
439 </assert_contents>
440 </output>
394 <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size"/> 441 <output name="anndata_out" file="pp.downsample_counts.random-randint.h5ad" ftype="h5ad" compare="sim_size"/>
395 </test> 442 </test>
396 </tests> 443 </tests>
397 <help><![CDATA[ 444 <help><![CDATA[
398 445