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 |
|---|---|
| date | Thu, 03 Oct 2024 22:42:14 +0000 |
| parents | 178242b82297 |
| children |
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| 18:38db3fef7aad | 19:cb43c5d3acd3 |
|---|---|
| 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 |