| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4+galaxy0 |
| scanpy_plot |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| scanpy | 1.10.2 | package |
| anndata | 0.10.3 | package |
| numpy | 1.26.4 | package |
| pandas | 2.2.2 | package |
| scipy | 1.14.1 | package |
| statsmodels | 0.14.2 | package |
| fa2 | 0.3.5 | package |
| matplotlib | 3.9.1 | package |
| seaborn | 0.13.2 | package |
| python-igraph | 0.11.6 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
adata: pbmc68k_reduced.h5ad format: png method|type|basis: umap method|type|color: HES4 method|type|type: basis method|use_raw: True method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|color_map: inferno method|plot|palette: inferno method|plot|size: 1 method|method: pl.scatter advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
| Test-2 |
adata: krumsiek11.h5ad format: png method|type|x: EKLF method|type|y: Cebpa method|type|type: xy method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|palette: bwr method|plot|size: 1 method|plot|title: A title method|method: pl.scatter advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-3 |
adata: pbmc68k_reduced.h5ad format: png method|type|x: n_genes method|type|y: n_counts method|type|type: xy method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|palette: bwr method|plot|size: 1 method|plot|title: A title method|method: pl.scatter advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
| Test-4 |
adata: krumsiek11.h5ad format: png method|groupby: cell_type method|dendrogram: True method|figsize|width: 10 method|figsize|height: 3 method|figsize|custom: yes method|swap_axes: True method|matplotlib_pyplot_imshow|cmap: YlGnBu method|method: pl.heatmap advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-5 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|var_names|var_names: Fog1,EKLF,SCL method|var_names|type: custom method|groupby: cell_type method|gene_symbols: symbol method|dendrogram: True method|figsize|width: 10 method|figsize|height: 3 method|figsize|custom: yes method|swap_axes: True method|show_gene_labels: True method|matplotlib_pyplot_imshow|cmap: YlGnBu method|method: pl.heatmap advanced_common|show_log: True |
name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-6 |
adata: pbmc68k_reduced.h5ad format: png method|var_names|var_names: CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402 method|var_names|type: custom method|groupby: louvain method|dendrogram: True method|var_group_positions_0|start: 0 method|var_group_positions_0|end: 1 method|var_group_positions_0|label: B cells method|var_group_positions_1|start: 11 method|var_group_positions_1|end: 12 method|var_group_positions_1|label: dendritic method|color_map: hot method|dot_max: 0.7 method|dot_min: 0.1 method|method: pl.dotplot advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
| Test-7 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|var_names|var_names: Fog1,EKLF,SCL method|var_names|type: custom method|groupby: cell_type method|gene_symbols: symbol method|dendrogram: True method|color_map: YlGnBu method|method: pl.dotplot advanced_common|show_log: True |
name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-8 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|groupby: cell_type method|gene_symbols: symbol method|dendrogram: True method|method: pl.tracksplot advanced_common|show_log: True |
name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-9 |
adata: pbmc68k_reduced.h5ad format: png method|key_variables|keys: n_genes, percent_mito, n_counts method|key_variables|type: custom method|violin_plot|multi_panel|multi_panel: True method|seaborn_violinplot|linewidth: 0 method|method: pl.violin advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
| Test-10 |
adata: krumsiek11.h5ad format: png method|groupby: cell_type method|dendrogram: True method|swap_axes: True method|violin_plot|density_norm: width method|seaborn_violinplot|linewidth: 0 method|method: pl.stacked_violin advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-11 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|var_names|var_names: Fog1,EKLF,SCL method|var_names|type: custom method|groupby: cell_type method|gene_symbols: symbol method|dendrogram: True method|swap_axes: True method|method: pl.stacked_violin advanced_common|show_log: True |
name: value name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-12 |
adata: krumsiek11.h5ad format: png method|groupby: cell_type method|dendrogram: True method|swap_axes: True method|method: pl.matrixplot advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-13 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|var_names|var_names: Fog1,EKLF,SCL method|var_names|type: custom method|groupby: cell_type method|gene_symbols: symbol method|dendrogram: True method|figsize|width: 10 method|figsize|height: 3 method|figsize|custom: yes method|method: pl.matrixplot advanced_common|show_log: True |
name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-14 |
adata: krumsiek11.h5ad format: png method|seaborn_clustermap|method: single method|seaborn_clustermap|col_cluster: False method|seaborn_clustermap|row_cluster: False method|method: pl.clustermap advanced_common|show_log: True |
name: value name: value |
krumsiek11.h5ad value |
| Test-15 |
adata: pp.filter_genes_dispersion.krumsiek11-seurat.h5ad format: png method|gene_symbols: symbol method|setseaborn_boxplot|color: blue method|setseaborn_boxplot|saturation: 0.5 method|method: pl.highest_expr_genes advanced_common|show_log: True |
name: value name: value |
pp.filter_genes_dispersion.krumsiek11-seurat.h5ad value |
| Test-16 |
adata: pp.highly_variable_genes.seurat.blobs.h5ad format: png method|method: pl.highly_variable_genes advanced_common|show_log: True |
name: value name: value |
pp.highly_variable_genes.seurat.blobs.h5ad value |
| Test-17 |
adata: pp.scrublet.krumsiek11.h5ad format: png method|method: pl.scrublet_score_distribution advanced_common|show_log: True |
name: value name: value |
pp.scrublet.krumsiek11.h5ad value |
| Test-18 |
adata: pbmc68k_reduced.h5ad format: pdf method|color: CD3D,CD79A method|gene_symbols: symbol method|plot|components_0|axis1: 1 method|plot|components_0|axis2: 2 method|plot|components_1|axis1: 1 method|plot|components_1|axis2: 3 method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|plot|ncols: 2 method|method: pl.pca advanced_common|show_log: True |
name: value name: value |
pbmc68k_reduced.h5ad value |
| Test-19 |
adata: pp.pca.krumsiek11.h5ad format: png method|components: 1,2,3 method|method: pl.pca_loadings advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
| Test-20 |
adata: pp.pca.krumsiek11.h5ad format: png method|method: pl.pca_variance_ratio advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
| Test-21 |
adata: pp.pca.krumsiek11.h5ad format: png method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|method: pl.pca_overview advanced_common|show_log: True |
name: value name: value |
pp.pca.krumsiek11.h5ad value |
| Test-22 |
adata: tl.tsne.krumsiek11.h5ad format: png method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|method: pl.tsne advanced_common|show_log: True |
name: value name: value |
tl.tsne.krumsiek11.h5ad value |
| Test-23 |
adata: tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad format: png method|color: paul15_clusters method|gene_symbols: symbol method|edges|edges: True method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|method: pl.umap advanced_common|show_log: True |
name: value name: value |
tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
| Test-24 |
adata: tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad format: png method|color: paul15_clusters method|gene_symbols: symbol method|plot|legend_fontsize: 1 method|plot|legend_fontweight: normal method|plot|size: 1 method|method: pl.diffmap advanced_common|show_log: True |
name: value name: value |
tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
| Test-25 |
adata: tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad format: png method|layout: fr method|edges|edges_color: Crimson method|edges|edges: True method|sort_order: False method|plot|legend_fontweight: normal method|method: pl.draw_graph advanced_common|show_log: True |
name: value name: value |
tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad value |
| Test-26 |
adata: tl.embedding_density.umap.pbmc68k_reduced.h5ad format: png method|key: umap_density_bulk_labels method|method: pl.embedding_density advanced_common|show_log: True |
name: value name: value |
tl.embedding_density.umap.pbmc68k_reduced.h5ad value |
| Test-27 |
adata: tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad format: png method|method: pl.dpt_timeseries advanced_common|show_log: True |
name: value name: value |
tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad value |
| Test-28 |
adata: tl.paga.neighbors.paul15_gauss_braycurtis.h5ad format: png method|threshold: 0.01 method|color: louvain method|layout: fr method|fontsize: 1 method|edge_width_scale: 5 method|method: pl.paga |
name: value name: value |
tl.paga.neighbors.paul15_gauss_braycurtis.h5ad value |
| Test-29 |
adata: tl.paga.neighbors.paul15_gauss_braycurtis.h5ad format: png method|threshold: 0.01 method|color: louvain method|layout: fr method|fontsize: 1 method|edge_width_scale: 5 method|method: pl.paga_compare |
name: value |
tl.paga.neighbors.paul15_gauss_braycurtis.h5ad value |
| Test-30 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|method: pl.rank_genes_groups advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-31 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|genes|n_genes: 10 method|genes|select: n_genes method|method: pl.rank_genes_groups_violin advanced_common|show_log: True |
name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-32 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|dendrogram: True method|swap_axes: True method|violin_plot|stripplot|jitter|size: 1 method|violin_plot|stripplot|jitter|jitter: True method|violin_plot|stripplot|stripplot: True method|violin_plot|density_norm: width method|method: pl.rank_genes_groups_stacked_violin advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-33 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|method: pl.rank_genes_groups_heatmap advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-34 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|method: pl.rank_genes_groups_dotplot advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-35 |
adata: tl.rank_genes_groups.krumsiek11.h5ad format: png method|n_genes: 10 method|method: pl.rank_genes_groups_matrixplot advanced_common|show_log: True |
name: value name: value |
tl.rank_genes_groups.krumsiek11.h5ad value |
| Test-36 |
adata: cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad format: png method|var_names|var_names: tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv method|var_names|type: customfile method|method: pl.rank_genes_groups_dotplot advanced_common|show_log: True |
name: value name: value |
cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv value |
| Test-37 |
adata: cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad format: png method|var_names|var_names: tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv method|var_names|type: customfile method|method: pl.rank_genes_groups_dotplot advanced_common|show_log: True |
name: value name: value |
cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv value |
| Test-38 |
adata: cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad format: png method|method: pl.rank_genes_groups_tracksplot advanced_common|show_log: True |
name: value name: value |
cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad value |