Merge pull request #4517 from pavanvidem/update-3k-pbmc

Update clustering 3k PBMCs tutorial with latest scanpy and anndata
galaxyproject · Dec 5, 2023 · c7dd5c3 · c7dd5c3
2 parents 4170822 + 0ec1eb7
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diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/dotplot_annotated_clusters.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/dotplot_annotated_clusters.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/pca_loadings.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/pca_loadings.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/plot_rank_genes_groups_heatmap.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/plot_rank_genes_groups_heatmap.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_t-test.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_t-test.png
diff --git a/...le-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_violin_wilcoxon_0_vs_1.png b/...le-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_violin_wilcoxon_0_vs_1.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_wilcoxon.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_wilcoxon.png
diff --git a/...cs/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_wilcoxon_0_vs_1.png b/...cs/single-cell/images/scrna-scanpy-pbmc3k/rank_genes_groups_wilcoxon_0_vs_1.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_after_clustering.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_after_clustering.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_annotated_clusters.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_annotated_clusters.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_before_clustering.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_before_clustering.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_plot_marker_genes.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/umap_plot_marker_genes.png
diff --git a/topics/single-cell/images/scrna-scanpy-pbmc3k/violin_plot_marker_genes.png b/topics/single-cell/images/scrna-scanpy-pbmc3k/violin_plot_marker_genes.png
diff --git a/...ell/images/scrna-scanpy-pbmc3k/violin_plot_rank_genes_groups_CST3_NKG7_PPBP.png b/...ell/images/scrna-scanpy-pbmc3k/violin_plot_rank_genes_groups_CST3_NKG7_PPBP.png
diff --git a/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md b/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/tutorial.md
diff --git a/...ngle-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy-test.yml b/...ngle-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy-test.yml
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+- doc: Test outline for Clustering-3k-PBMC-with-Scanpy
+  job:
+    Barcodes:
+      class: File
+      path: https://zenodo.org/record/3581213/files/barcodes.tsv
+      filetype: txt
+    Genes:
+      class: File
+      path: https://zenodo.org/record/3581213/files/genes.tsv
+      filetype: tabular
+    Matrix:
+      class: File
+      path: https://zenodo.org/record/3581213/files/matrix.mtx
+      filetype: mtx
+    mito header:
+      class: File
+      path: test-data/mito header.tabular
+      filetype: tabular
+  outputs:
+    out_png:
+      path: test-data/out_png.png
+    out_png (Step 31):
+      path: test-data/out_png (Step 31).png
+    out_png (Step 39):
+      path: test-data/out_png (Step 39).png
+    uns_rank_genes_groups_names:
+      path: test-data/uns_rank_genes_groups_names.tabular
+    out_png (Step 35):
+      path: test-data/out_png (Step 35).png
+    out_png (Step 38):
+      path: test-data/out_png (Step 38).png
+    out_svg:
+      path: test-data/out_svg.svg
+    collection_png:
+      element_tests:
+        louvain_0:
+          path: test-data/collection_png_louvain_0.png