| Previous changeset 10:aa0c474463c2 (2021-09-22) Next changeset 12:9b0cdb8cf6be (2023-11-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d |
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modified:
macros.xml plot.xml test-data/blobs.h5ad test-data/krumsiek11.h5ad test-data/pbmc68k_reduced.h5ad test-data/pl.clustermap.krumsiek11.png test-data/pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.dotplot.krumsiek11.png test-data/pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.draw_graph.png test-data/pl.heatmap.krumsiek11.png test-data/pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png test-data/pl.highly_variable_genes.seurat.blobs.png test-data/pl.matrixplot.krumsiek11.png test-data/pl.paga.paul15_gauss_braycurtis.png test-data/pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf test-data/pl.pca_loadings.pp.pca.krumsiek11.png test-data/pl.pca_overview.pp.pca.krumsiek11.png test-data/pl.pca_variance_ratio.pp.pca.krumsiek11.png test-data/pl.rank_genes_groups.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png test-data/pl.rank_genes_groups_violin.Ery.png test-data/pl.rank_genes_groups_violin.Mk.png test-data/pl.rank_genes_groups_violin.Mo.png test-data/pl.rank_genes_groups_violin.Neu.png test-data/pl.rank_genes_groups_violin.progenitor.png test-data/pl.scatter.krumsiek11.png test-data/pl.scatter.umap.pbmc68k_reduced.png test-data/pl.stacked_violin.krumsiek11.png test-data/pl.tsne.krumsiek11.png test-data/pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png test-data/pl.violin.pbmc68k_reduced_custom.png test-data/pp.calculate_qc_metrics.sparce_csr_matrix.h5ad test-data/pp.combat.blobs.h5ad test-data/pp.downsample_counts.random-randint.h5ad test-data/pp.filter_cells.krumsiek11-max_genes.h5ad test-data/pp.filter_cells.krumsiek11-min_counts.h5ad test-data/pp.filter_genes.krumsiek11-min_counts.h5ad test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad test-data/pp.highly_variable_genes.seurat.blobs.h5ad test-data/pp.log1p.krumsiek11.h5ad test-data/pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.normalize_total.krumsiek11.h5ad test-data/pp.pca.krumsiek11.h5ad test-data/pp.pca.krumsiek11_chunk.h5ad test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.updated.h5ad test-data/pp.recipe_zheng17.random-randint.h5ad test-data/pp.regress_out.krumsiek11.h5ad test-data/pp.scale.krumsiek11.h5ad test-data/pp.scale_max_value.krumsiek11.h5ad test-data/pp.sqrt.krumsiek11.h5ad test-data/pp.subsample.krumsiek11_fraction.h5ad test-data/pp.subsample.krumsiek11_n_obs.h5ad test-data/sparce_csr_matrix.h5ad test-data/tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.leiden.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.louvain.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.pca.krumsiek11.h5ad test-data/tl.rank_genes_groups.krumsiek11.h5ad test-data/tl.rank_genes_groups.liblinear.krumsiek11.h5ad test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad test-data/tl.score_genes.krumsiek11.h5ad test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad test-data/tl.tsne.krumsiek11.h5ad test-data/tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad |
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added:
test-data/pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png test-data/pl.embedding_density.pbmc68k_reduced.png test-data/pl.paga_compare.paul15_gauss_braycurtis.png test-data/pl.scatter.pbmc68k_reduced.png test-data/tl.embedding_density.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad test-data/tl.paga.neighbors.paul15_gauss_braycurtis.h5ad |
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| diff -r aa0c474463c2 -r 95777145cb92 macros.xml --- a/macros.xml Wed Sep 22 21:13:39 2021 +0000 +++ b/macros.xml Wed Nov 08 14:47:20 2023 +0000 |
| [ |
| @@ -1,12 +1,16 @@ <macros> - <token name="@version@">1.7.1</token> - <token name="@profile@">19.01</token> + <token name="@version@">1.9.6</token> + <token name="@profile@">22.05</token> <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@version@">scanpy</requirement> - <requirement type="package" version="2.0.17">loompy</requirement> - <requirement type="package" version="0.8.3">leidenalg</requirement> + <requirement type="package" version="3.0.6">loompy</requirement> + <requirement type="package" version="0.10.1">leidenalg</requirement> + <requirement type="package" version="0.8.1">louvain</requirement> + <requirement type="package" version="1.5.3">pandas</requirement> + <requirement type="package" version="3.7">matplotlib</requirement> + <requirement type="package" version="0.12.2">seaborn</requirement> <yield /> </requirements> </xml> @@ -15,9 +19,15 @@ <xref type="bio.tools">scanpy</xref> </xrefs> </xml> + <xml name="creators"> + <creator> + <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" /> + </creator> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-017-1382-0</citation> + <citation type="doi">10.1093/gigascience/giaa102</citation> </citations> </xml> <xml name="version_command"> @@ -56,7 +66,7 @@ <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> </xml> <token name="@CMD_read_inputs@"><![CDATA[ -adata = sc.read('anndata.h5ad') +adata = sc.read_h5ad('anndata.h5ad') ]]> </token> <xml name="inputs_common_advanced"> @@ -66,12 +76,12 @@ </xml> <xml name="anndata_outputs"> <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> - <data name="hidden_output" format="txt" label="Log file" > + <data name="hidden_output" format="txt" label="Log file" > <filter>advanced_common['show_log']</filter> </data> </xml> <token name="@CMD_anndata_write_outputs@"><![CDATA[ -adata.write('anndata.h5ad') +adata.write_h5ad('anndata.h5ad') with open('anndata_info.txt','w', encoding='utf-8') as ainfo: print(adata, file=ainfo) ]]> @@ -875,7 +885,7 @@ </xml> <xml name="param_color_map"> <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> - <option value="None">Default</option> + <option value="" >Default</option> <expand macro="matplotlib_pyplot_colormap"/> </param> </xml> @@ -979,7 +989,7 @@ @CMD_param_legend_fontsize@ legend_fontweight='$method.plot.legend_fontweight', @CMD_param_size@ - #if str($method.plot.color_map) != 'None' + #if str($method.plot.color_map) != '' color_map='$method.plot.color_map', #end if #if str($method.plot.palette) != '' |
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| diff -r aa0c474463c2 -r 95777145cb92 plot.xml --- a/plot.xml Wed Sep 22 21:13:39 2021 +0000 +++ b/plot.xml Wed Nov 08 14:47:20 2023 +0000 |
| [ |
| b'@@ -1,9 +1,9 @@\n-<tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">\n+<tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@">\n <description> with scanpy</description>\n- <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <stdio>\n <regex match="... storing" source="stderr" level="warning"/>\n@@ -21,11 +21,32 @@\n \n #if $method.method == \'pl.scatter\'\n \n+#if $method.type.type == \'xy\':\n+x_field=\'$method.type.x\'\n+y_field=\'$method.type.y\'\n+\n+#if $method.type.log:\n+if x_field in adata.obs or x_field in adata.var:\n+ if x_field in adata.obs:\n+ adata.obs[f"log_{x_field}"] = np.log10(adata.obs[x_field])\n+ elif x_field in adata.var:\n+ adata.var[f"log_{x_field}"] = np.log10(adata.var[x_field])\n+ x_field=f"log_{x_field}"\n+\n+if y_field in adata.obs or y_field in adata.var:\n+ if y_field in adata.obs:\n+ adata.obs[f"log_{y_field}"] = np.log10(adata.obs[y_field])\n+ elif y_field in adata.var:\n+ adata.var[f"log_{y_field}"] = np.log10(adata.var[y_field])\n+ y_field=f"log_{y_field}"\n+#end if\n+#end if\n+\n sc.pl.scatter(\n @CMD_param_plot_inputs@\n- #if $method.type.type == \'xy\'\n- x=\'$method.type.x\',\n- y=\'$method.type.y\',\n+ #if $method.type.type == \'xy\':\n+ x=x_field,\n+ y=y_field,\n #if str($method.type.color) != \'\'\n color=\'$method.type.color\',\n \t #end if\n@@ -265,6 +286,29 @@\n @CMD_pl_attribute_section@\n @CMD_params_matplotlib_pyplot_scatter@)\n \n+#else if $method.method == \'pl.embedding_density\'\n+sc.pl.embedding_density(\n+ @CMD_param_plot_inputs@\n+ basis=\'$method.basis\',\n+ #if str($method.key) != \'\'\n+ key=\'$method.key\',\n+ #end if\n+ #if str($method.groupby) != \'\'\n+ groupby=\'$method.groupby\',\n+ #end if\n+ #if str($method.group) != \'\'\n+ #set $group = ([x.strip() for x in str($method.group).split(\',\')])\n+ group=$group,\n+ #end if\n+ #if str($method.color_map) != \'\'\n+ color_map=\'$method.color_map\',\n+ #end if\n+ bg_dotsize=$method.bg_dotsize,\n+ fg_dotsize=$method.fg_dotsize,\n+ ncols=$method.ncols,\n+ wspace=$method.wspace,\n+ hspace=$method.hspace)\n+\n #else if $method.method == \'pl.dpt_groups_pseudotime\'\n sc.pl.dpt_groups_pseudotime(\n @CMD_param_plot_inputs@\n@@ -305,7 +349,7 @@\n #set $annotations=([x.strip() for x in str($method.annotations).split(\',\')])\n annotations=$annotations,\n #end if\n- #if str($method.color_map) != \'\'\n+ #if str($method.color_map) != \'None\'\n color_map=\'$method.color_map\',\n #end if\n n_avg=$method.n_avg,\n@@ -358,6 +402,9 @@\n sc.pl.rank_genes_groups_dotplot(\n @CMD_param_plot_inputs@\n @CMD_pl_rank_genes_groups_ext@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_params_plots@\n @CMD_pl_dotplot@)\n \n@@ -366,6 +413,9 @@\n @CMD_param_plot_inputs@\n @CMD_pl_rank_genes_groups_ext@\n @CMD_params_plots@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_pl_heatmap@)\n \n #else if $method.method == \'pl.rank_genes_groups_matrixplot\'\n@@ -373,6 +423,9 @@\n @CMD_param_plot_inputs@\n @CMD_pl_rank_genes_groups_ext@\n @CMD_params_plots@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_pl_matrixplot@)\n \n #else if $method.method == \'pl.rank_genes_groups_stacked_violin\'\n@@ -380,6 +433,9 @@\n @CMD_param_plot_inputs@\n @CMD_pl_rank_genes_groups_ext@\n @CMD_params_plots@\n+ #if str($method.gene_symbols) != \'\'\n+ gene_symbols=\'$method.gene_symbols\',\n+ #end if\n @CMD_pl_stacked_violin@)\n \n #end if\n@@ -397,7 +453,6 @@\n <option value="pl.stacked_violin">Generic: Stacked violin plots, using \'pl.stacked_violin\'</option>\n <option value="pl.matrixplot">Generic: Heatmap of the '..b'ml>`__\n \n \n Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)\n@@ -2231,56 +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/@version@/api/scanpy.pl.paga.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.paga_compare.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.paga_path.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups_violin.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups_dotplot.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups_heatmap.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups_matrixplot.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/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/@version@/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |
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