| Previous changeset 10:c5d3684f7c4c (2021-09-22) Next changeset 12:3081ff5c84a3 (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:
inspect.xml macros.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 c5d3684f7c4c -r 6bd82ed14acd inspect.xml --- a/inspect.xml Wed Sep 22 21:14:32 2021 +0000 +++ b/inspect.xml Wed Nov 08 14:48:14 2023 +0000 |
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| b'@@ -1,6 +1,5 @@\n <tool id="scanpy_inspect" name="Inspect and manipulate" version="@galaxy_version@" profile="@profile@">\n <description> with scanpy</description>\n- <expand macro="bio_tools"/>\n <macros>\n <import>macros.xml</import>\n <xml name="score_genes_params">\n@@ -51,6 +50,7 @@\n label="The seed of the pseudo random number generator to use when shuffling the data" help=""/>\n </xml>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <expand macro="version_command"/>\n <command detect_errors="exit_code"><![CDATA[\n@@ -453,7 +453,8 @@\n </when>\n </conditional>\n </when>\n- <!--<when value="tl.marker_gene_overlap">\n+ <!-- With inplace=True, NotImplementedError: Writing Pandas dataframes to h5ad is currently under development. Please use `inplace=False`. -->\n+ <!-- <when value="tl.marker_gene_overlap">\n <repeat name="reference_markers" title="Marker genes">\n <param name="key" type="text" value="" label="Cell identity name" help=""/>\n <param name="values" type="text" value="" label="List of genes" help="Comma-separated names from \'var\'"/>\n@@ -477,7 +478,7 @@\n </conditional>\n <param argument="top_n_markers" type="integer" optional="true" label="Number of top data-derived marker genes to use" help="By default all calculated marker genes are used. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/>\n <param argument="adj_pval_threshold" type="float" optional="true" label="Significance threshold on the adjusted p-values to select marker genes" help=" This can only be used when adjusted p-values are calculated by \'tl.rank_genes_groups\'. If adj_pval_threshold is set along with top_n_markers, then adj_pval_threshold is ignored."/>\n- <param argument="key_added" type="text" value="" optional="true" label="Key that will contain the marker overlap scores in \'uns\'"/>\n+ <param argument="key_added" type="text" value="marker_gene_overlap" optional="true" label="Key that will contain the marker overlap scores in \'uns\'"/>\n </when>-->\n <when value="pp.log1p"/>\n <when value="pp.scale">\n@@ -494,8 +495,8 @@\n <expand macro="anndata_outputs"/>\n </outputs>\n <tests>\n- <test>\n- <!-- test 0 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 1 -->\n <param name="adata" value="sparce_csr_matrix.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.calculate_qc_metrics"/>\n@@ -517,8 +518,8 @@\n </output>\n <output name="anndata_out" file="pp.calculate_qc_metrics.sparce_csr_matrix.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n- <test>\n- <!-- test 1 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 2 -->\n <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.neighbors"/>\n@@ -547,8 +548,8 @@\n </assert_contents>\n </output>\n </test>\n- <test>\n- <!-- test 2 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 3 -->\n <param name="adata" value="pp.recipe_weinreb17.paul15_subsample.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.neighbors"/>\n@@ -572,8 +573,8 @@\n </output>\n <output name="anndata_out" file="pp.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n- <test>\n- <!-- test 3 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 4 -->\n <param name="a'..b' <conditional name="method">\n <param name="method" value="pp.scale"/>\n@@ -832,8 +833,8 @@\n </output>\n <output name="anndata_out" file="pp.scale.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n- <test>\n- <!-- test 10 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 12 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.scale"/>\n@@ -852,8 +853,8 @@\n </output>\n <output name="anndata_out" file="pp.scale_max_value.krumsiek11.h5ad" ftype="h5ad" compare="sim_size"/>\n </test>\n- <test>\n- <!-- test 11 -->\n+ <test expect_num_outputs="2">\n+ <!-- test 13 -->\n <param name="adata" value="krumsiek11.h5ad" />\n <conditional name="method">\n <param name="method" value="pp.sqrt"/>\n@@ -892,7 +893,7 @@\n - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in)\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.calculate_qc_metrics.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__\n \n Compute a neighborhood graph of observations, using `pp.neighbors`\n ==================================================================\n@@ -911,7 +912,7 @@\n This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.neighbors.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.neighbors.html>`__\n \n Score a set of genes, using `tl.score_genes`\n ============================================\n@@ -924,7 +925,7 @@\n for Scanpy by Davide Cittaro.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes.html>`__\n \n Score cell cycle genes, using `tl.score_genes_cell_cycle`\n =========================================================\n@@ -934,7 +935,7 @@\n `score_genes` for more explanation.\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.score_genes_cell_cycle.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__\n \n Rank genes for characterizing groups, using `tl.rank_genes_groups`\n ==================================================================\n@@ -950,7 +951,7 @@\n This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.rank_genes_groups.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.rank_genes_groups.html>`__\n \n \n Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)\n@@ -963,13 +964,13 @@\n =========================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.log1p.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.log1p.html>`__\n \n Scale data to unit variance and zero mean (`pp.scale`)\n ======================================================\n \n More details on the `scanpy documentation\n-<https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.scale.html>`__\n+<https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.scale.html>`__\n \n Computes the square root the data matrix (`pp.sqrt`)\n ====================================================\n' |
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| diff -r c5d3684f7c4c -r 6bd82ed14acd macros.xml --- a/macros.xml Wed Sep 22 21:14:32 2021 +0000 +++ b/macros.xml Wed Nov 08 14:48:14 2023 +0000 |
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| @@ -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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