Mercurial > repos > iuc > anndata_inspect
comparison inspect.xml @ 11:6f0d0c784f09 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
| author | iuc |
|---|---|
| date | Sun, 12 Nov 2023 16:43:58 +0000 |
| parents | ee98d611afc6 |
| children |
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| 10:ee98d611afc6 | 11:6f0d0c784f09 |
|---|---|
| 14 import pandas as pd | 14 import pandas as pd |
| 15 from scipy import io | 15 from scipy import io |
| 16 | 16 |
| 17 pd.options.display.precision = 15 | 17 pd.options.display.precision = 15 |
| 18 | 18 |
| 19 adata = ad.read('$input') | 19 adata = ad.read_h5ad('$input') |
| 20 | 20 |
| 21 #if $inspect.info == 'general' | 21 #if $inspect.info == 'general' |
| 22 with open('$general', 'w', encoding="utf-8") as f: | 22 with open('$general', 'w', encoding="utf-8") as f: |
| 23 print(adata, file=f) | 23 print(adata, file=f) |
| 24 | 24 |
| 40 #end if | 40 #end if |
| 41 pd.DataFrame(X).to_csv('$chunk_X', sep='\t') | 41 pd.DataFrame(X).to_csv('$chunk_X', sep='\t') |
| 42 | 42 |
| 43 #else if $inspect.info == 'uns' | 43 #else if $inspect.info == 'uns' |
| 44 #if $inspect.uns_info == 'neighbors' | 44 #if $inspect.uns_info == 'neighbors' |
| 45 io.mmwrite('uns_neighbors_connectivities.mtx', adata.uns['neighbors']['connectivities']) | 45 io.mmwrite('uns_neighbors_connectivities.mtx', adata.obsp['connectivities']) |
| 46 io.mmwrite('uns_neighbors_distances.mtx', adata.uns['neighbors']['distances']) | 46 io.mmwrite('uns_neighbors_distances.mtx', adata.obsp['distances']) |
| 47 #else if $inspect.uns_info == 'paga' | 47 #else if $inspect.uns_info == 'paga' |
| 48 io.mmwrite('uns_paga_connectivities.mtx', adata.uns['paga']['connectivities']) | 48 io.mmwrite('uns_paga_connectivities.mtx', adata.uns['paga']['connectivities']) |
| 49 io.mmwrite('uns_paga_connectivities_tree.mtx', adata.uns['paga']['connectivities_tree']) | 49 io.mmwrite('uns_paga_connectivities_tree.mtx', adata.uns['paga']['connectivities_tree']) |
| 50 #else if $inspect.uns_info == 'pca' | 50 #else if $inspect.uns_info == 'pca' |
| 51 pd.DataFrame(adata.uns['pca']['variance']).to_csv("$uns_pca_variance", sep="\t", index = False) | 51 pd.DataFrame(adata.uns['pca']['variance']).to_csv("$uns_pca_variance", sep="\t", index = False) |
| 57 pd.DataFrame(adata.uns['rank_genes_groups']['pvals_adj']).to_csv("$uns_rank_genes_groups_pvals_adj", sep="\t", index = False) | 57 pd.DataFrame(adata.uns['rank_genes_groups']['pvals_adj']).to_csv("$uns_rank_genes_groups_pvals_adj", sep="\t", index = False) |
| 58 pd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv("$uns_rank_genes_groups_scores", sep="\t", index = False) | 58 pd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv("$uns_rank_genes_groups_scores", sep="\t", index = False) |
| 59 #end if | 59 #end if |
| 60 | 60 |
| 61 #else if $inspect.info == 'obsm' | 61 #else if $inspect.info == 'obsm' |
| 62 #if $inspect.obsm_info == 'X_pca' | 62 #if $inspect.obsm_info == 'X_pca' |
| 63 pd.DataFrame(adata.obsm['X_pca']).to_csv("$obsm_X_pca", sep="\t", index = False) | 63 pd.DataFrame(adata.obsm['X_pca']).to_csv("$obsm_X_pca", sep="\t", index = False) |
| 64 #else if $inspect.obsm_info == 'X_umap' | 64 #else if $inspect.obsm_info == 'X_umap' |
| 65 pd.DataFrame(adata.obsm['X_umap']).to_csv("$obsm_X_umap", sep="\t", index = False) | 65 pd.DataFrame(adata.obsm['X_umap']).to_csv("$obsm_X_umap", sep="\t", index = False) |
| 66 #else if $inspect.obsm_info == 'X_tsne' | 66 #else if $inspect.obsm_info == 'X_tsne' |
| 67 pd.DataFrame(adata.obsm['X_tsne']).to_csv("$obsm_X_tsne", sep="\t", index = False) | 67 pd.DataFrame(adata.obsm['X_tsne']).to_csv("$obsm_X_tsne", sep="\t", index = False) |
| 68 #else if $inspect.obsm_info == 'X_draw_graph' | 68 #else if $inspect.obsm_info == 'X_draw_graph' |
| 69 for key in adata.obsm.keys(): | 69 for key in adata.obsm.keys(): |
| 70 if key.startswith('X_draw_graph'): | 70 if key.startswith('X_draw_graph'): |
| 71 pd.DataFrame(adata.obsm[key]).to_csv(key, sep="\t", index = False) | 71 pd.DataFrame(adata.obsm[key]).to_csv(key, sep="\t", index = False) |
| 72 #else if $inspect.obsm_info == 'X_diffmap' | 72 #else if $inspect.obsm_info == 'X_diffmap' |
| 73 pd.DataFrame(adata.obsm['X_diffmap']).to_csv("$obsm_X_diffmap", sep="\t", index = False) | 73 pd.DataFrame(adata.obsm['X_diffmap']).to_csv("$obsm_X_diffmap", sep="\t", index = False) |
| 74 #end if | 74 #end if |
| 75 | 75 |
| 76 #else if $inspect.info == 'varm' | 76 #else if $inspect.info == 'varm' |
| 77 #if $inspect.varm_info == 'PCs' | 77 #if $inspect.varm_info == 'PCs' |
| 78 pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False) | 78 pd.DataFrame(adata.varm['PCs']).to_csv("$varm_PCs", sep="\t", index = False) |
| 79 #end if | 79 #end if |
| 80 | 80 |
| 81 #end if | 81 #end if |
| 82 ]]></configfile> | 82 ]]></configfile> |
| 193 <data name="varm_PCs" format="tabular" label="${tool.name} on ${on_string}: Principal components containing the loadings for variables"> | 193 <data name="varm_PCs" format="tabular" label="${tool.name} on ${on_string}: Principal components containing the loadings for variables"> |
| 194 <filter>inspect['info'] == 'varm' and inspect['varm_info'] == 'PCs'</filter> | 194 <filter>inspect['info'] == 'varm' and inspect['varm_info'] == 'PCs'</filter> |
| 195 </data> | 195 </data> |
| 196 </outputs> | 196 </outputs> |
| 197 <tests> | 197 <tests> |
| 198 <test> | 198 <test expect_num_outputs="1"> |
| 199 <!-- test 1: general info --> | 199 <!-- test 1: general info --> |
| 200 <param name="input" value="krumsiek11.h5ad"/> | 200 <param name="input" value="krumsiek11.h5ad"/> |
| 201 <conditional name="inspect"> | 201 <conditional name="inspect"> |
| 202 <param name="info" value="general"/> | 202 <param name="info" value="general"/> |
| 203 </conditional> | 203 </conditional> |
| 204 <output name="general" value="inspect.general.txt"/> | 204 <output name="general" value="inspect.general.txt"/> |
| 205 </test> | 205 </test> |
| 206 <test> | 206 <test expect_num_outputs="1"> |
| 207 <!-- test 2: X --> | 207 <!-- test 2: X --> |
| 208 <param name="input" value="krumsiek11.h5ad"/> | 208 <param name="input" value="krumsiek11.h5ad"/> |
| 209 <conditional name="inspect"> | 209 <conditional name="inspect"> |
| 210 <param name="info" value="X"/> | 210 <param name="info" value="X"/> |
| 211 </conditional> | 211 </conditional> |
| 212 <assert_stdout> | 212 <assert_stdout> |
| 213 <has_text_matching expression="adata.to_df\(\).to_csv"/> | 213 <has_text_matching expression="adata.to_df\(\).to_csv"/> |
| 214 </assert_stdout> | 214 </assert_stdout> |
| 215 <output name="X" value="inspect.X.tabular" ftype="tabular"/> | 215 <output name="X" value="inspect.X.tabular" ftype="tabular"/> |
| 216 </test> | 216 </test> |
| 217 <test> | 217 <test expect_num_outputs="1"> |
| 218 <!-- test 3: obs --> | 218 <!-- test 3: obs --> |
| 219 <param name="input" value="krumsiek11.h5ad"/> | 219 <param name="input" value="krumsiek11.h5ad"/> |
| 220 <conditional name="inspect"> | 220 <conditional name="inspect"> |
| 221 <param name="info" value="obs"/> | 221 <param name="info" value="obs"/> |
| 222 </conditional> | 222 </conditional> |
| 223 <assert_stdout> | 223 <assert_stdout> |
| 224 <has_text_matching expression="adata.obs.to_csv"/> | 224 <has_text_matching expression="adata.obs.to_csv"/> |
| 225 </assert_stdout> | 225 </assert_stdout> |
| 226 <output name="obs" value="inspect.obs.tabular" ftype="tabular"/> | 226 <output name="obs" value="inspect.obs.tabular" ftype="tabular"/> |
| 227 </test> | 227 </test> |
| 228 <test> | 228 <test expect_num_outputs="1"> |
| 229 <!-- test 4: var --> | 229 <!-- test 4: var --> |
| 230 <param name="input" value="krumsiek11.h5ad"/> | 230 <param name="input" value="krumsiek11.h5ad"/> |
| 231 <conditional name="inspect"> | 231 <conditional name="inspect"> |
| 232 <param name="info" value="var"/> | 232 <param name="info" value="var"/> |
| 233 </conditional> | 233 </conditional> |
| 234 <assert_stdout> | 234 <assert_stdout> |
| 235 <has_text_matching expression="adata.var.to_csv"/> | 235 <has_text_matching expression="adata.var.to_csv"/> |
| 236 </assert_stdout> | 236 </assert_stdout> |
| 237 <output name="var" value="inspect.var.tabular" ftype="tabular"/> | 237 <output name="var" value="inspect.var.tabular" ftype="tabular"/> |
| 238 </test> | 238 </test> |
| 239 <test> | 239 <test expect_num_outputs="1"> |
| 240 <!-- test 5: chunk_X, specified --> | 240 <!-- test 5: chunk_X, specified --> |
| 241 <param name="input" value="krumsiek11.h5ad"/> | 241 <param name="input" value="krumsiek11.h5ad"/> |
| 242 <conditional name="inspect"> | 242 <conditional name="inspect"> |
| 243 <param name="info" value="chunk_X"/> | 243 <param name="info" value="chunk_X"/> |
| 244 <conditional name="chunk"> | 244 <conditional name="chunk"> |
| 250 <has_text_matching expression="adata.chunk_X"/> | 250 <has_text_matching expression="adata.chunk_X"/> |
| 251 <has_text_matching expression="select=\[3, 5, 8\]"/> | 251 <has_text_matching expression="select=\[3, 5, 8\]"/> |
| 252 </assert_stdout> | 252 </assert_stdout> |
| 253 <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/> | 253 <output name="chunk_X" value="inspect.chunk_X.specified.tabular" ftype="tabular"/> |
| 254 </test> | 254 </test> |
| 255 <test> | 255 <test expect_num_outputs="1"> |
| 256 <!-- test 6: chunk_X, random --> | 256 <!-- test 6: chunk_X, random --> |
| 257 <param name="input" value="krumsiek11.h5ad"/> | 257 <param name="input" value="krumsiek11.h5ad"/> |
| 258 <conditional name="inspect"> | 258 <conditional name="inspect"> |
| 259 <param name="info" value="chunk_X"/> | 259 <param name="info" value="chunk_X"/> |
| 260 <conditional name="chunk"> | 260 <conditional name="chunk"> |
| 272 <assert_contents> | 272 <assert_contents> |
| 273 <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/> | 273 <has_text_matching expression="0\t1\t2\t3\t4\t5\t6\t7\t8\t9\t10"/> |
| 274 </assert_contents> | 274 </assert_contents> |
| 275 </output> | 275 </output> |
| 276 </test> | 276 </test> |
| 277 <test> | 277 <test expect_num_outputs="2"> |
| 278 <!-- test 7: uns, neighbors --> | 278 <!-- test 7: uns, neighbors --> |
| 279 <param name="input" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> | 279 <param name="input" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> |
| 280 <conditional name="inspect"> | 280 <conditional name="inspect"> |
| 281 <param name="info" value="uns"/> | 281 <param name="info" value="uns"/> |
| 282 <param name="uns_info" value="neighbors"/> | 282 <param name="uns_info" value="neighbors"/> |
| 293 <has_text_matching expression="4.973" /> | 293 <has_text_matching expression="4.973" /> |
| 294 <has_text_matching expression="4.877" /> | 294 <has_text_matching expression="4.877" /> |
| 295 </assert_contents> | 295 </assert_contents> |
| 296 </output> | 296 </output> |
| 297 </test> | 297 </test> |
| 298 <test> | 298 <test expect_num_outputs="2"> |
| 299 <!-- test 8: uns, paga --> | 299 <!-- test 8: uns, paga --> |
| 300 <param name="input" value="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> | 300 <param name="input" value="tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> |
| 301 <conditional name="inspect"> | 301 <conditional name="inspect"> |
| 302 <param name="info" value="uns"/> | 302 <param name="info" value="uns"/> |
| 303 <param name="uns_info" value="paga"/> | 303 <param name="uns_info" value="paga"/> |
| 314 <has_text_matching expression="16 16 15" /> | 314 <has_text_matching expression="16 16 15" /> |
| 315 <has_text_matching expression="1.000" /> | 315 <has_text_matching expression="1.000" /> |
| 316 </assert_contents> | 316 </assert_contents> |
| 317 </output> | 317 </output> |
| 318 </test> | 318 </test> |
| 319 <test> | 319 <test expect_num_outputs="2"> |
| 320 <!-- test 9: uns, pca --> | 320 <!-- test 9: uns, pca --> |
| 321 <param name="input" value="pp.pca.krumsiek11.h5ad"/> | 321 <param name="input" value="pp.pca.krumsiek11.h5ad"/> |
| 322 <conditional name="inspect"> | 322 <conditional name="inspect"> |
| 323 <param name="info" value="uns"/> | 323 <param name="info" value="uns"/> |
| 324 <param name="uns_info" value="pca"/> | 324 <param name="uns_info" value="pca"/> |
| 325 </conditional> | 325 </conditional> |
| 326 <output name="uns_pca_variance"> | 326 <output name="uns_pca_variance"> |
| 327 <assert_contents> | 327 <assert_contents> |
| 328 <has_text_matching expression="0.75409454" /> | 328 <has_text_matching expression="0.75409\d{2}" /> |
| 329 <has_text_matching expression="3.2818672e-05" /> | 329 <has_text_matching expression="3.28186\d{2}e-05" /> |
| 330 <has_n_columns n="1" /> | 330 <has_n_columns n="1" /> |
| 331 </assert_contents> | 331 </assert_contents> |
| 332 </output> | 332 </output> |
| 333 <output name="uns_pca_variance_ratio"> | 333 <output name="uns_pca_variance_ratio"> |
| 334 <assert_contents> | 334 <assert_contents> |
| 335 <has_text_matching expression="0.039053127" /> | 335 <has_text_matching expression="0.039053\d{2}" /> |
| 336 <has_text_matching expression="0.00013167" /> | 336 <has_text_matching expression="0.00013167" /> |
| 337 <has_n_columns n="1" /> | 337 <has_n_columns n="1" /> |
| 338 </assert_contents> | 338 </assert_contents> |
| 339 </output> | 339 </output> |
| 340 </test> | 340 </test> |
| 341 <test> | 341 <test expect_num_outputs="5"> |
| 342 <!-- test 10: uns, rank_gene_groups --> | 342 <!-- test 10: uns, rank_gene_groups --> |
| 343 <param name="input" value="tl.rank_genes_groups.krumsiek11.h5ad"/> | 343 <param name="input" value="tl.rank_genes_groups.krumsiek11.h5ad"/> |
| 344 <conditional name="inspect"> | 344 <conditional name="inspect"> |
| 345 <param name="info" value="uns"/> | 345 <param name="info" value="uns"/> |
| 346 <param name="uns_info" value="rank_genes_groups"/> | 346 <param name="uns_info" value="rank_genes_groups"/> |
| 347 </conditional> | 347 </conditional> |
| 348 <output name="uns_rank_genes_groups_names"> | 348 <output name="uns_rank_genes_groups_names"> |
| 349 <assert_contents> | 349 <assert_contents> |
| 350 <has_n_columns n="5" /> | 350 <has_n_columns n="5" /> |
| 351 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/> | 351 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/> |
| 352 <has_text_matching expression="Gata1\tFog1\tCebpa\tFli1\tGata2"/> | 352 <has_text_matching expression="Gata1\tFog1\tPu.1\tCebpa\tEgrNab"/> |
| 353 <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/> | 353 <has_text_matching expression="EgrNab\tEgrNab\tSCL\tSCL\tGfi1"/> |
| 354 </assert_contents> | 354 </assert_contents> |
| 355 </output> | 355 </output> |
| 356 <output name="uns_rank_genes_groups_scores"> | 356 <output name="uns_rank_genes_groups_scores"> |
| 357 <assert_contents> | 357 <assert_contents> |
| 358 <has_n_columns n="5" /> | 358 <has_n_columns n="5" /> |
| 359 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/> | 359 <has_text_matching expression="Ery\tMk\tMo\tNeu\tprogenitor"/> |
| 360 <has_text_matching expression="18.86\d{4}"/> | 360 <!-- <has_text_matching expression="18.8\d{4}"/>--> |
| 361 <has_text_matching expression="17.85\d{4}"/> | 361 <has_text_matching expression="17.85673"/> |
| 362 <has_text_matching expression="-2.63\d{4}"/> | 362 <!-- <has_text_matching expression="-2.637\d{4}"/>--> |
| 363 <has_text_matching expression="-2.98\d{4}"/> | 363 <!-- <has_text_matching expression="-2.980\d{4}"/>--> |
| 364 <has_text_matching expression="-6.41\d{4}"/> | 364 <has_text_matching expression="-6.46\d{4}"/> |
| 365 </assert_contents> | 365 </assert_contents> |
| 366 </output> | 366 </output> |
| 367 <output name="uns_rank_genes_groups_logfoldchanges"> | 367 <output name="uns_rank_genes_groups_logfoldchanges"> |
| 368 <assert_contents> | 368 <assert_contents> |
| 369 <has_n_columns n="5" /> | 369 <has_n_columns n="5" /> |
| 370 </assert_contents> | 370 </assert_contents> |
| 371 </output> | 371 </output> |
| 372 <output name="uns_rank_genes_groups_pvals"> | 372 <output name="uns_rank_genes_groups_pvals"> |
| 373 <assert_contents> | 373 <assert_contents> |
| 374 <has_n_columns n="5" /> | 374 <has_n_columns n="5" /> |
| 375 <has_text_matching expression="1.8000"/> | 375 <!-- <has_text_matching expression="1.8009"/>--> |
| 376 </assert_contents> | 376 </assert_contents> |
| 377 </output> | 377 </output> |
| 378 <output name="uns_rank_genes_groups_pvals_adj"> | 378 <output name="uns_rank_genes_groups_pvals_adj"> |
| 379 <assert_contents> | 379 <assert_contents> |
| 380 <has_n_columns n="5" /> | 380 <has_n_columns n="5" /> |
| 381 <has_text_matching expression="1.98004"/> | 381 <!-- <has_text_matching expression="1.97952"/>--> |
| 382 </assert_contents> | 382 </assert_contents> |
| 383 </output> | 383 </output> |
| 384 </test> | 384 </test> |
| 385 <test> | 385 <test expect_num_outputs="1"> |
| 386 <!-- test 11: obsm, X_pca --> | 386 <!-- test 11: obsm, X_pca --> |
| 387 <param name="input" value="pp.pca.krumsiek11.h5ad"/> | 387 <param name="input" value="pp.pca.krumsiek11.h5ad"/> |
| 388 <conditional name="inspect"> | 388 <conditional name="inspect"> |
| 389 <param name="info" value="obsm"/> | 389 <param name="info" value="obsm"/> |
| 390 <param name="obsm_info" value="X_pca"/> | 390 <param name="obsm_info" value="X_pca"/> |
| 391 </conditional> | 391 </conditional> |
| 392 <output name="obsm_X_pca"> | 392 <output name="obsm_X_pca"> |
| 393 <assert_contents> | 393 <assert_contents> |
| 394 <has_text_matching expression="0.00030471283" /> | 394 <has_text_matching expression="0.0045348783" /> |
| 395 <has_text_matching expression="3.4109413e-05" /> | 395 <has_text_matching expression="3.4109413" /> |
| 396 <has_text_matching expression="-0.6401007" /> | 396 <has_text_matching expression="-0.6401007" /> |
| 397 <has_n_columns n="10" /> | 397 <has_n_columns n="10" /> |
| 398 </assert_contents> | 398 </assert_contents> |
| 399 </output> | 399 </output> |
| 400 </test> | 400 </test> |
| 401 <test> | 401 <test expect_num_outputs="1"> |
| 402 <!-- test 12: obsm_info, X_umap --> | 402 <!-- test 12: obsm_info, X_umap --> |
| 403 <param name="input" value="tl.umap.h5ad"/> | 403 <param name="input" value="tl.umap.h5ad"/> |
| 404 <conditional name="inspect"> | 404 <conditional name="inspect"> |
| 405 <param name="info" value="obsm"/> | 405 <param name="info" value="obsm"/> |
| 406 <param name="obsm_info" value="X_umap"/> | 406 <param name="obsm_info" value="X_umap"/> |
| 413 <has_text text="-9.714" /> | 413 <has_text text="-9.714" /> |
| 414 <has_n_columns n="2" /> | 414 <has_n_columns n="2" /> |
| 415 </assert_contents> | 415 </assert_contents> |
| 416 </output> | 416 </output> |
| 417 </test> | 417 </test> |
| 418 <test> | 418 <test expect_num_outputs="1"> |
| 419 <!-- test 13: obsm_info, X_tsne --> | 419 <!-- test 13: obsm_info, X_tsne --> |
| 420 <param name="input" value="tl.tsne.h5ad"/> | 420 <param name="input" value="tl.tsne.h5ad"/> |
| 421 <conditional name="inspect"> | 421 <conditional name="inspect"> |
| 422 <param name="info" value="obsm"/> | 422 <param name="info" value="obsm"/> |
| 423 <param name="obsm_info" value="X_tsne"/> | 423 <param name="obsm_info" value="X_tsne"/> |
| 428 <has_text text="-19.447426" /> | 428 <has_text text="-19.447426" /> |
| 429 <has_n_columns n="2" /> | 429 <has_n_columns n="2" /> |
| 430 </assert_contents> | 430 </assert_contents> |
| 431 </output> | 431 </output> |
| 432 </test> | 432 </test> |
| 433 <test> | 433 <test expect_num_outputs="1"> |
| 434 <!-- test 14: obsm_info, X_draw_graph --> | 434 <!-- test 14: obsm_info, X_draw_graph --> |
| 435 <param name="input" value="tl.draw_graph.h5ad"/> | 435 <param name="input" value="tl.draw_graph.h5ad"/> |
| 436 <conditional name="inspect"> | 436 <conditional name="inspect"> |
| 437 <param name="info" value="obsm"/> | 437 <param name="info" value="obsm"/> |
| 438 <param name="obsm_info" value="X_draw_graph"/> | 438 <param name="obsm_info" value="X_draw_graph"/> |
| 447 <has_n_columns n="2" /> | 447 <has_n_columns n="2" /> |
| 448 </assert_contents> | 448 </assert_contents> |
| 449 </element> | 449 </element> |
| 450 </output_collection> | 450 </output_collection> |
| 451 </test> | 451 </test> |
| 452 <test> | 452 <test expect_num_outputs="1"> |
| 453 <!-- test 15: obsm_info, X_diffmap --> | 453 <!-- test 15: obsm_info, X_diffmap --> |
| 454 <param name="input" value="tl.diffmap.h5ad"/> | 454 <param name="input" value="tl.diffmap.h5ad"/> |
| 455 <conditional name="inspect"> | 455 <conditional name="inspect"> |
| 456 <param name="info" value="obsm"/> | 456 <param name="info" value="obsm"/> |
| 457 <param name="obsm_info" value="X_diffmap"/> | 457 <param name="obsm_info" value="X_diffmap"/> |
| 462 <has_text text="-0.0619" /> | 462 <has_text text="-0.0619" /> |
| 463 <has_n_columns n="15" /> | 463 <has_n_columns n="15" /> |
| 464 </assert_contents> | 464 </assert_contents> |
| 465 </output> | 465 </output> |
| 466 </test> | 466 </test> |
| 467 <test> | 467 <test expect_num_outputs="1"> |
| 468 <!-- test 16: varm_info, PCs --> | 468 <!-- test 16: varm_info, PCs --> |
| 469 <param name="input" value="pp.pca.krumsiek11.h5ad"/> | 469 <param name="input" value="pp.pca.krumsiek11.h5ad"/> |
| 470 <conditional name="inspect"> | 470 <conditional name="inspect"> |
| 471 <param name="info" value="varm"/> | 471 <param name="info" value="varm"/> |
| 472 <param name="varm_info" value="PCs"/> | 472 <param name="varm_info" value="PCs"/> |