Mercurial > repos > iuc > scanpy_cluster_reduce_dimension
comparison cluster_reduce_dimension.xml @ 19:cb43c5d3acd3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
author | iuc |
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date | Thu, 03 Oct 2024 22:42:14 +0000 |
parents | 178242b82297 |
children |
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18:38db3fef7aad | 19:cb43c5d3acd3 |
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222 ) | 222 ) |
223 | 223 |
224 #end if | 224 #end if |
225 | 225 |
226 @CMD_ANNDATA_WRITE_OUTPUTS@ | 226 @CMD_ANNDATA_WRITE_OUTPUTS@ |
227 ]]> | 227 ]]> |
228 </configfile> | 228 </configfile> |
229 </configfiles> | 229 </configfiles> |
230 <inputs> | 230 <inputs> |
231 <expand macro="inputs_anndata"/> | 231 <expand macro="inputs_anndata"/> |
232 <conditional name="method"> | 232 <conditional name="method"> |
477 <has_h5_keys keys="obsm/X_pca"/> | 477 <has_h5_keys keys="obsm/X_pca"/> |
478 <has_h5_keys keys="varm/PCs"/> | 478 <has_h5_keys keys="varm/PCs"/> |
479 </assert_contents> | 479 </assert_contents> |
480 </output> | 480 </output> |
481 </test> | 481 </test> |
482 | 482 |
483 <!-- test 5 --> | 483 <!-- test 5 --> |
484 <test expect_num_outputs="2"> | 484 <test expect_num_outputs="2"> |
485 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> | 485 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> |
486 <conditional name="method"> | 486 <conditional name="method"> |
487 <param name="method" value="tl.diffmap"/> | 487 <param name="method" value="tl.diffmap"/> |
499 <has_h5_keys keys="obsm/X_diffmap"/> | 499 <has_h5_keys keys="obsm/X_diffmap"/> |
500 <has_h5_keys keys="uns/diffmap_evals"/> | 500 <has_h5_keys keys="uns/diffmap_evals"/> |
501 </assert_contents> | 501 </assert_contents> |
502 </output> | 502 </output> |
503 </test> | 503 </test> |
504 | 504 |
505 <!-- test 6 --> | 505 <!-- test 6 --> |
506 <test expect_num_outputs="2"> | 506 <test expect_num_outputs="2"> |
507 <param name="adata" value="krumsiek11.h5ad"/> | 507 <param name="adata" value="krumsiek11.h5ad"/> |
508 <conditional name="method"> | 508 <conditional name="method"> |
509 <param name="method" value="tl.tsne"/> | 509 <param name="method" value="tl.tsne"/> |
527 <has_h5_keys keys="uns/tsne"/> | 527 <has_h5_keys keys="uns/tsne"/> |
528 <has_h5_keys keys="obsm/X_tsne"/> | 528 <has_h5_keys keys="obsm/X_tsne"/> |
529 </assert_contents> | 529 </assert_contents> |
530 </output> | 530 </output> |
531 </test> | 531 </test> |
532 | 532 |
533 <!-- test 7 --> | 533 <!-- test 7 --> |
534 <test expect_num_outputs="2"> | 534 <test expect_num_outputs="2"> |
535 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> | 535 <param name="adata" value="pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> |
536 <conditional name="method"> | 536 <conditional name="method"> |
537 <param name="method" value="tl.umap"/> | 537 <param name="method" value="tl.umap"/> |
579 </assert_contents> | 579 </assert_contents> |
580 </output> | 580 </output> |
581 <output name="anndata_out" ftype="h5ad"> | 581 <output name="anndata_out" ftype="h5ad"> |
582 <assert_contents> | 582 <assert_contents> |
583 <has_h5_keys keys="uns/draw_graph"/> | 583 <has_h5_keys keys="uns/draw_graph"/> |
584 <has_h5_keys keys="obsm/X_draw_graph_fr"/> | 584 <has_h5_keys keys="obsm/X_draw_graph_fa"/> |
585 </assert_contents> | 585 </assert_contents> |
586 </output> | 586 </output> |
587 </test> | 587 </test> |
588 | 588 |
589 <!-- test 9 --> | 589 <!-- test 9 --> |
613 </assert_contents> | 613 </assert_contents> |
614 </output> | 614 </output> |
615 </test> | 615 </test> |
616 | 616 |
617 <!-- test 10 --> | 617 <!-- test 10 --> |
618 <test expect_num_outputs="2"> | 618 <test expect_num_outputs="2"> |
619 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> | 619 <param name="adata" value="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> |
620 <conditional name="method"> | 620 <conditional name="method"> |
621 <param name="method" value="tl.paga"/> | 621 <param name="method" value="tl.paga"/> |
622 <param name="groups" value="paul15_clusters"/> | 622 <param name="groups" value="paul15_clusters"/> |
623 </conditional> | 623 </conditional> |
663 </assert_contents> | 663 </assert_contents> |
664 </output> | 664 </output> |
665 </test> | 665 </test> |
666 </tests> | 666 </tests> |
667 <help><![CDATA[ | 667 <help><![CDATA[ |
668 | 668 |
669 Cluster cells into subgroups (`tl.louvain`) | 669 Cluster cells into subgroups (`tl.louvain`) |
670 =========================================== | 670 =========================================== |
671 | 671 |
672 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation | 672 Cluster cells using the Louvain algorithm (Blondel et al, 2008) in the implementation |
673 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell | 673 of Traag et al,2017. The Louvain algorithm has been proposed for single-cell |