moved under anndata parent

galaxyproject · Apr 18, 2024 · 8f4b2e7 · 8f4b2e7
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diff --git a/tools/anndata/.shed.yml b/tools/anndata/.shed.yml
@@ -1,6 +1,6 @@
 name: anndata
 owner: iuc
-description: "Import, Export, Inspect and Manipulate Anndata and Loom objects"
+description: "Import, Export, Inspect, Operate on and Manipulate Anndata and Loom objects"
 homepage_url: https://anndata.readthedocs.io
 long_description: |
     AnnData provides a scalable way of keeping track of data together with learned annotations. It is used within Scanpy, for which it was initially developed. Loompy is a similar method of dealing with hd5 files, containing layers of matrices with the same row and column attributes. Information on loompy is is available at: <http://loompy.org>
@@ -14,6 +14,6 @@ auto_tool_repositories:
   description_template: "Wrapper for the anndata tool suite: {{ tool_name }}"
 suite:
   name: "suite_anndata"
-  description: "Import, Export, Inspect and Manipulate Anndata and Loom objects"
+  description: "Import, Export, Inspect, Operate on and Manipulate Anndata and Loom objects"
   long_description: |
     AnnData provides a scalable way of keeping track of data together with learned annotations. It is used within Scanpy, for which it was initially developed. Loompy is a similar method of dealing with hd5 files, containing layers of matrices with the same row and column attributes. Information on loompy is is available at: <http://loompy.org>
diff --git a/tools/anndata_ops/anndata_ops.xml → tools/anndata/anndata_ops.xml b/tools/anndata_ops/anndata_ops.xml → tools/anndata/anndata_ops.xml
diff --git a/tools/anndata_ops/test-data/anndata_ops.h5 → tools/anndata/test-data/anndata_ops.h5 b/tools/anndata_ops/test-data/anndata_ops.h5 → tools/anndata/test-data/anndata_ops.h5
diff --git a/...ndata_ops/test-data/anndata_ops_xlayer.h5 → ...s/anndata/test-data/anndata_ops_xlayer.h5 b/...ndata_ops/test-data/anndata_ops_xlayer.h5 → ...s/anndata/test-data/anndata_ops_xlayer.h5
diff --git a/tools/anndata_ops/test-data/barcodes.tsv → tools/anndata/test-data/barcodes.tsv b/tools/anndata_ops/test-data/barcodes.tsv → tools/anndata/test-data/barcodes.tsv
diff --git a/tools/anndata_ops/test-data/bbknn.h5 → tools/anndata/test-data/bbknn.h5 b/tools/anndata_ops/test-data/bbknn.h5 → tools/anndata/test-data/bbknn.h5
diff --git a/tools/anndata_ops/test-data/bbknn_copy.h5 → tools/anndata/test-data/bbknn_copy.h5 b/tools/anndata_ops/test-data/bbknn_copy.h5 → tools/anndata/test-data/bbknn_copy.h5
diff --git a/tools/anndata_ops/test-data/combat_copy.h5 → tools/anndata/test-data/combat_copy.h5 b/tools/anndata_ops/test-data/combat_copy.h5 → tools/anndata/test-data/combat_copy.h5
diff --git a/tools/anndata_ops/test-data/compute_graph.h5 → tools/anndata/test-data/compute_graph.h5 b/tools/anndata_ops/test-data/compute_graph.h5 → tools/anndata/test-data/compute_graph.h5
diff --git a/tools/anndata_ops/test-data/diffexp.tsv → tools/anndata/test-data/diffexp.tsv b/tools/anndata_ops/test-data/diffexp.tsv → tools/anndata/test-data/diffexp.tsv
diff --git a/tools/anndata_ops/test-data/diffmap.h5 → tools/anndata/test-data/diffmap.h5 b/tools/anndata_ops/test-data/diffmap.h5 → tools/anndata/test-data/diffmap.h5
diff --git a/tools/anndata_ops/test-data/filter_cells.h5 → tools/anndata/test-data/filter_cells.h5 b/tools/anndata_ops/test-data/filter_cells.h5 → tools/anndata/test-data/filter_cells.h5
diff --git a/tools/anndata_ops/test-data/filter_genes.h5 → tools/anndata/test-data/filter_genes.h5 b/tools/anndata_ops/test-data/filter_genes.h5 → tools/anndata/test-data/filter_genes.h5
diff --git a/tools/anndata_ops/test-data/find_cluster.h5 → tools/anndata/test-data/find_cluster.h5 b/tools/anndata_ops/test-data/find_cluster.h5 → tools/anndata/test-data/find_cluster.h5
diff --git a/tools/anndata_ops/test-data/find_cluster.tsv → tools/anndata/test-data/find_cluster.tsv b/tools/anndata_ops/test-data/find_cluster.tsv → tools/anndata/test-data/find_cluster.tsv
diff --git a/...data_ops/test-data/find_variable_genes.h5 → .../anndata/test-data/find_variable_genes.h5 b/...data_ops/test-data/find_variable_genes.h5 → .../anndata/test-data/find_variable_genes.h5
diff --git a/tools/anndata_ops/test-data/genes.tsv → tools/anndata/test-data/genes.tsv b/tools/anndata_ops/test-data/genes.tsv → tools/anndata/test-data/genes.tsv
diff --git a/tools/anndata_ops/test-data/groupby.txt → tools/anndata/test-data/groupby.txt b/tools/anndata_ops/test-data/groupby.txt → tools/anndata/test-data/groupby.txt
diff --git a/tools/anndata_ops/test-data/harmony_copy.h5 → tools/anndata/test-data/harmony_copy.h5 b/tools/anndata_ops/test-data/harmony_copy.h5 → tools/anndata/test-data/harmony_copy.h5
diff --git a/tools/anndata_ops/test-data/louvain_1.0 → tools/anndata/test-data/louvain_1.0 b/tools/anndata_ops/test-data/louvain_1.0 → tools/anndata/test-data/louvain_1.0
diff --git a/tools/anndata_ops/test-data/louvain_1.0.tsv → tools/anndata/test-data/louvain_1.0.tsv b/tools/anndata_ops/test-data/louvain_1.0.tsv → tools/anndata/test-data/louvain_1.0.tsv
diff --git a/tools/anndata_ops/test-data/matrix.mtx → tools/anndata/test-data/matrix.mtx b/tools/anndata_ops/test-data/matrix.mtx → tools/anndata/test-data/matrix.mtx
diff --git a/tools/anndata_ops/test-data/mnn.h5 → tools/anndata/test-data/mnn.h5 b/tools/anndata_ops/test-data/mnn.h5 → tools/anndata/test-data/mnn.h5
diff --git a/tools/anndata_ops/test-data/mnn_copy.h5 → tools/anndata/test-data/mnn_copy.h5 b/tools/anndata_ops/test-data/mnn_copy.h5 → tools/anndata/test-data/mnn_copy.h5
diff --git a/tools/anndata_ops/test-data/n_neighbors.txt → tools/anndata/test-data/n_neighbors.txt b/tools/anndata_ops/test-data/n_neighbors.txt → tools/anndata/test-data/n_neighbors.txt
diff --git a/...s/anndata_ops/test-data/normalise_data.h5 → tools/anndata/test-data/normalise_data.h5 b/...s/anndata_ops/test-data/normalise_data.h5 → tools/anndata/test-data/normalise_data.h5
diff --git a/tools/anndata_ops/test-data/paga.h5 → tools/anndata/test-data/paga.h5 b/tools/anndata_ops/test-data/paga.h5 → tools/anndata/test-data/paga.h5
diff --git a/tools/anndata_ops/test-data/paga_compare.png → tools/anndata/test-data/paga_compare.png b/tools/anndata_ops/test-data/paga_compare.png → tools/anndata/test-data/paga_compare.png
diff --git a/tools/anndata_ops/test-data/perplexity.txt → tools/anndata/test-data/perplexity.txt b/tools/anndata_ops/test-data/perplexity.txt → tools/anndata/test-data/perplexity.txt
diff --git a/tools/anndata_ops/test-data/perplexity_1.txt → tools/anndata/test-data/perplexity_1.txt b/tools/anndata_ops/test-data/perplexity_1.txt → tools/anndata/test-data/perplexity_1.txt
diff --git a/...s/anndata_ops/test-data/perplexity_10.txt → tools/anndata/test-data/perplexity_10.txt b/...s/anndata_ops/test-data/perplexity_10.txt → tools/anndata/test-data/perplexity_10.txt
diff --git a/tools/anndata_ops/test-data/perplexity_5.txt → tools/anndata/test-data/perplexity_5.txt b/tools/anndata_ops/test-data/perplexity_5.txt → tools/anndata/test-data/perplexity_5.txt
diff --git a/tools/anndata_ops/test-data/plot_embed.png → tools/anndata/test-data/plot_embed.png b/tools/anndata_ops/test-data/plot_embed.png → tools/anndata/test-data/plot_embed.png
diff --git a/...s/anndata_ops/test-data/plot_scrublet.png → tools/anndata/test-data/plot_scrublet.png b/...s/anndata_ops/test-data/plot_scrublet.png → tools/anndata/test-data/plot_scrublet.png
diff --git a/tools/anndata_ops/test-data/read_10x.h5 → tools/anndata/test-data/read_10x.h5 b/tools/anndata_ops/test-data/read_10x.h5 → tools/anndata/test-data/read_10x.h5
diff --git a/tools/anndata_ops/test-data/resolution.txt → tools/anndata/test-data/resolution.txt b/tools/anndata_ops/test-data/resolution.txt → tools/anndata/test-data/resolution.txt
diff --git a/...data_ops/test-data/run_fdg.embeddings.tsv → .../anndata/test-data/run_fdg.embeddings.tsv b/...data_ops/test-data/run_fdg.embeddings.tsv → .../anndata/test-data/run_fdg.embeddings.tsv
diff --git a/...data_ops/test-data/run_pca.embeddings.tsv → .../anndata/test-data/run_pca.embeddings.tsv b/...data_ops/test-data/run_pca.embeddings.tsv → .../anndata/test-data/run_pca.embeddings.tsv
diff --git a/tools/anndata_ops/test-data/run_pca.h5 → tools/anndata/test-data/run_pca.h5 b/tools/anndata_ops/test-data/run_pca.h5 → tools/anndata/test-data/run_pca.h5
diff --git a/...ata_ops/test-data/run_tsne.embeddings.tsv → ...anndata/test-data/run_tsne.embeddings.tsv b/...ata_ops/test-data/run_tsne.embeddings.tsv → ...anndata/test-data/run_tsne.embeddings.tsv
diff --git a/...ata_ops/test-data/run_umap.embeddings.tsv → ...anndata/test-data/run_umap.embeddings.tsv b/...ata_ops/test-data/run_umap.embeddings.tsv → ...anndata/test-data/run_umap.embeddings.tsv
diff --git a/tools/anndata_ops/test-data/run_umap.h5 → tools/anndata/test-data/run_umap.h5 b/tools/anndata_ops/test-data/run_umap.h5 → tools/anndata/test-data/run_umap.h5
diff --git a/tools/anndata_ops/test-data/scale_data.h5 → tools/anndata/test-data/scale_data.h5 b/tools/anndata_ops/test-data/scale_data.h5 → tools/anndata/test-data/scale_data.h5
diff --git a/tools/anndata_ops/test-data/scrublet.h5 → tools/anndata/test-data/scrublet.h5 b/tools/anndata_ops/test-data/scrublet.h5 → tools/anndata/test-data/scrublet.h5
diff --git a/...ps/test-data/test_incomplete_metadata.tsv → ...ta/test-data/test_incomplete_metadata.tsv b/...ps/test-data/test_incomplete_metadata.tsv → ...ta/test-data/test_incomplete_metadata.tsv