| Previous changeset 4:cb18f2388815 (2019-12-18) Next changeset 6:dbbe1ea8ecb1 (2020-02-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85" |
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modified:
plot.xml |
| b |
| diff -r cb18f2388815 -r 8599fd07d140 plot.xml --- a/plot.xml Wed Dec 18 15:57:48 2019 -0500 +++ b/plot.xml Mon Feb 10 05:25:58 2020 -0500 |
| b |
| b'@@ -1778,7 +1778,7 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.matrixplot.html>`__\n \n Generic: Hierarchically-clustered heatmap (`pl.clustermap`)\n ===========================================================\n@@ -1796,7 +1796,7 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/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@@ -1808,7 +1808,7 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.highest_expr_genes.html>`__\n \n Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)\n ===================================================================================\n@@ -1816,25 +1816,25 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.pca_variance_ratio.html>`__\n \n PCA: Plot PCA results (`pl.pca_overview`)\n =========================================\n@@ -1843,37 +1843,37 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.umap.html>`__\n \n Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)\n ==============================================================\n \n More details on the '..b'ml>`__\n \n \n Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)\n@@ -1886,56 +1886,56 @@\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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/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://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |