| Previous changeset 13:6f5349dd5c49 (2024-03-14) Next changeset 15:70fa84e99463 (2024-07-31) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de |
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modified:
macros.xml plot.xml |
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| diff -r 6f5349dd5c49 -r f7446fd8d5e7 macros.xml --- a/macros.xml Thu Mar 14 15:35:53 2024 +0000 +++ b/macros.xml Sat May 18 18:32:22 2024 +0000 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.9.6</token> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@profile@">22.05</token> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@profile@">21.09</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> |
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| diff -r 6f5349dd5c49 -r f7446fd8d5e7 plot.xml --- a/plot.xml Thu Mar 14 15:35:53 2024 +0000 +++ b/plot.xml Sat May 18 18:32:22 2024 +0000 |
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| b'@@ -2299,7 +2299,7 @@\n category.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.matrixplot.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__\n \n Generic: Hierarchically-clustered heatmap (`pl.clustermap`)\n ===========================================================\n@@ -2317,7 +2317,7 @@\n Column indices, use: clustergrid.dendrogram_col.reordered_ind\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.clustermap.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__\n \n Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)\n =========================================================================================================\n@@ -2329,7 +2329,7 @@\n This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highest_expr_genes.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__\n \n Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)\n ===================================================================================\n@@ -2337,25 +2337,25 @@\n It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.highly_variable_genes.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__\n \n PCA: Scatter plot in PCA coordinates (`pl.pca`)\n ===============================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__\n \n PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)\n =====================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_loadings.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__\n \n PCA: Plot the variance ratio (`pl.pca_variance_ratio`)\n ======================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_variance_ratio.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__\n \n PCA: Plot PCA results (`pl.pca_overview`)\n =========================================\n@@ -2364,37 +2364,37 @@\n if you want to change the default settings.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.pca_overview.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__\n \n Embedding: Scatter plot in tSNE basis (`pl.tsne`)\n =================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.tsne.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__\n \n Embeddings: Scatter plot in UMAP basis (`pl.umap`)\n ==================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.umap.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__\n \n Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)\n ==============================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/s'..b'ble/api/generated/scanpy.pl.dpt_timeseries.html>`__\n \n \n Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)\n@@ -2407,56 +2407,56 @@\n `maxiter` parameter by 1 if the layout is flipped.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__\n \n \n Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)\n ==========================================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_compare.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__\n \n Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)\n ======================================================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.paga_path.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__\n \n Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)\n ===============================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__\n \n Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)\n ==================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_violin.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__\n \n Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)\n ====================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_dotplot.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__\n \n Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)\n ====================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_heatmap.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__\n \n Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)\n ==========================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__\n \n Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)\n ==================================================================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |