From 8f4b2e770b4ccb9e2cb4fcd7aa50352d30fece6c Mon Sep 17 00:00:00 2001 From: Mehmet Tekman Date: Thu, 18 Apr 2024 17:02:23 +0200 Subject: [PATCH] moved under anndata parent --- tools/anndata/.shed.yml | 4 ++-- tools/{anndata_ops => anndata}/anndata_ops.xml | 0 .../test-data/anndata_ops.h5 | Bin .../test-data/anndata_ops_xlayer.h5 | Bin .../{anndata_ops => anndata}/test-data/barcodes.tsv | 0 tools/{anndata_ops => anndata}/test-data/bbknn.h5 | Bin .../test-data/bbknn_copy.h5 | Bin .../test-data/combat_copy.h5 | Bin .../test-data/compute_graph.h5 | Bin .../{anndata_ops => anndata}/test-data/diffexp.tsv | 0 tools/{anndata_ops => anndata}/test-data/diffmap.h5 | Bin .../test-data/filter_cells.h5 | Bin .../test-data/filter_genes.h5 | Bin .../test-data/find_cluster.h5 | Bin .../test-data/find_cluster.tsv | 0 .../test-data/find_variable_genes.h5 | Bin tools/{anndata_ops => anndata}/test-data/genes.tsv | 0 .../{anndata_ops => anndata}/test-data/groupby.txt | 0 .../test-data/harmony_copy.h5 | Bin .../{anndata_ops => anndata}/test-data/louvain_1.0 | Bin .../test-data/louvain_1.0.tsv | 0 tools/{anndata_ops => anndata}/test-data/matrix.mtx | 0 tools/{anndata_ops => anndata}/test-data/mnn.h5 | Bin .../{anndata_ops => anndata}/test-data/mnn_copy.h5 | Bin .../test-data/n_neighbors.txt | 0 .../test-data/normalise_data.h5 | Bin tools/{anndata_ops => anndata}/test-data/paga.h5 | Bin .../test-data/paga_compare.png | Bin .../test-data/perplexity.txt | 0 .../test-data/perplexity_1.txt | 0 .../test-data/perplexity_10.txt | 0 .../test-data/perplexity_5.txt | 0 .../test-data/plot_embed.png | Bin .../test-data/plot_scrublet.png | Bin .../{anndata_ops => anndata}/test-data/read_10x.h5 | Bin .../test-data/resolution.txt | 0 .../test-data/run_fdg.embeddings.tsv | 0 .../test-data/run_pca.embeddings.tsv | 0 tools/{anndata_ops => anndata}/test-data/run_pca.h5 | Bin .../test-data/run_tsne.embeddings.tsv | 0 .../test-data/run_umap.embeddings.tsv | 0 .../{anndata_ops => anndata}/test-data/run_umap.h5 | Bin .../test-data/scale_data.h5 | Bin .../{anndata_ops => anndata}/test-data/scrublet.h5 | Bin .../test-data/test_incomplete_metadata.tsv | 0 45 files changed, 2 insertions(+), 2 deletions(-) rename tools/{anndata_ops => anndata}/anndata_ops.xml (100%) rename tools/{anndata_ops => anndata}/test-data/anndata_ops.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/anndata_ops_xlayer.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/barcodes.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/bbknn.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/bbknn_copy.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/combat_copy.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/compute_graph.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/diffexp.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/diffmap.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/filter_cells.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/filter_genes.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/find_cluster.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/find_cluster.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/find_variable_genes.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/genes.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/groupby.txt (100%) rename tools/{anndata_ops => anndata}/test-data/harmony_copy.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/louvain_1.0 (100%) rename tools/{anndata_ops => anndata}/test-data/louvain_1.0.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/matrix.mtx (100%) rename tools/{anndata_ops => anndata}/test-data/mnn.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/mnn_copy.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/n_neighbors.txt (100%) rename tools/{anndata_ops => anndata}/test-data/normalise_data.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/paga.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/paga_compare.png (100%) rename tools/{anndata_ops => anndata}/test-data/perplexity.txt (100%) rename tools/{anndata_ops => anndata}/test-data/perplexity_1.txt (100%) rename tools/{anndata_ops => anndata}/test-data/perplexity_10.txt (100%) rename tools/{anndata_ops => anndata}/test-data/perplexity_5.txt (100%) rename tools/{anndata_ops => anndata}/test-data/plot_embed.png (100%) rename tools/{anndata_ops => anndata}/test-data/plot_scrublet.png (100%) rename tools/{anndata_ops => anndata}/test-data/read_10x.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/resolution.txt (100%) rename tools/{anndata_ops => anndata}/test-data/run_fdg.embeddings.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/run_pca.embeddings.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/run_pca.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/run_tsne.embeddings.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/run_umap.embeddings.tsv (100%) rename tools/{anndata_ops => anndata}/test-data/run_umap.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/scale_data.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/scrublet.h5 (100%) rename tools/{anndata_ops => anndata}/test-data/test_incomplete_metadata.tsv (100%) diff --git a/tools/anndata/.shed.yml b/tools/anndata/.shed.yml index 3aaf041efbf..dfd172f7034 100644 --- 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: @@ -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: diff --git a/tools/anndata_ops/anndata_ops.xml b/tools/anndata/anndata_ops.xml similarity index 100% rename from tools/anndata_ops/anndata_ops.xml rename to tools/anndata/anndata_ops.xml diff --git a/tools/anndata_ops/test-data/anndata_ops.h5 b/tools/anndata/test-data/anndata_ops.h5 similarity index 100% rename from tools/anndata_ops/test-data/anndata_ops.h5 rename to tools/anndata/test-data/anndata_ops.h5 diff --git a/tools/anndata_ops/test-data/anndata_ops_xlayer.h5 b/tools/anndata/test-data/anndata_ops_xlayer.h5 similarity index 100% rename from tools/anndata_ops/test-data/anndata_ops_xlayer.h5 rename to tools/anndata/test-data/anndata_ops_xlayer.h5 diff --git a/tools/anndata_ops/test-data/barcodes.tsv b/tools/anndata/test-data/barcodes.tsv similarity index 100% rename from tools/anndata_ops/test-data/barcodes.tsv rename to tools/anndata/test-data/barcodes.tsv diff --git a/tools/anndata_ops/test-data/bbknn.h5 b/tools/anndata/test-data/bbknn.h5 similarity index 100% rename from tools/anndata_ops/test-data/bbknn.h5 rename to tools/anndata/test-data/bbknn.h5 diff --git a/tools/anndata_ops/test-data/bbknn_copy.h5 b/tools/anndata/test-data/bbknn_copy.h5 similarity index 100% rename from tools/anndata_ops/test-data/bbknn_copy.h5 rename to tools/anndata/test-data/bbknn_copy.h5 diff --git a/tools/anndata_ops/test-data/combat_copy.h5 b/tools/anndata/test-data/combat_copy.h5 similarity index 100% rename from tools/anndata_ops/test-data/combat_copy.h5 rename to tools/anndata/test-data/combat_copy.h5 diff --git a/tools/anndata_ops/test-data/compute_graph.h5 b/tools/anndata/test-data/compute_graph.h5 similarity index 100% rename from tools/anndata_ops/test-data/compute_graph.h5 rename to tools/anndata/test-data/compute_graph.h5 diff --git a/tools/anndata_ops/test-data/diffexp.tsv b/tools/anndata/test-data/diffexp.tsv similarity index 100% rename from tools/anndata_ops/test-data/diffexp.tsv rename to tools/anndata/test-data/diffexp.tsv diff --git a/tools/anndata_ops/test-data/diffmap.h5 b/tools/anndata/test-data/diffmap.h5 similarity index 100% rename from tools/anndata_ops/test-data/diffmap.h5 rename to tools/anndata/test-data/diffmap.h5 diff --git a/tools/anndata_ops/test-data/filter_cells.h5 b/tools/anndata/test-data/filter_cells.h5 similarity index 100% rename from tools/anndata_ops/test-data/filter_cells.h5 rename to tools/anndata/test-data/filter_cells.h5 diff --git a/tools/anndata_ops/test-data/filter_genes.h5 b/tools/anndata/test-data/filter_genes.h5 similarity index 100% rename from tools/anndata_ops/test-data/filter_genes.h5 rename to tools/anndata/test-data/filter_genes.h5 diff --git a/tools/anndata_ops/test-data/find_cluster.h5 b/tools/anndata/test-data/find_cluster.h5 similarity index 100% rename from tools/anndata_ops/test-data/find_cluster.h5 rename to tools/anndata/test-data/find_cluster.h5 diff --git a/tools/anndata_ops/test-data/find_cluster.tsv 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tools/anndata/test-data/test_incomplete_metadata.tsv