| Previous changeset 16:c0a80a16560f (2024-08-20) Next changeset 18:d1cd8c147809 (2024-09-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb |
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modified:
README.md inspect.xml macros.xml test-data/cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.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.embedding_density.pbmc68k_reduced.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.paga_compare.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.newton-cg.pbmc68k_highly_reduced_marker_1.png test-data/pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.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.pbmc68k_reduced.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.recipe_zheng17.random-randint.h5ad test-data/random-randint.h5ad test-data/sparce_csr_matrix.h5ad test-data/tl.embedding_density.umap.pbmc68k_reduced.h5ad test-data/tl.rank_genes_groups.newton-cg.pbmc68k_reduced.h5ad |
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test-data/external.pp.bbknn.krumsiek11.h5ad test-data/pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png test-data/pl.scrublet_score_distribution.png test-data/pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png test-data/pp.pca.krumsiek11.batch.h5ad test-data/pp.scrublet.krumsiek11.h5ad |
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removed:
test-data/external.pp.magic.all_genes.krumsiek11.h5ad test-data/external.pp.magic.pca_only.krumsiek11.h5ad test-data/pp.calculate_qc_metrics.sparce_csr_matrix.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.filter_rank_genes_groups.h5ad test-data/pp.highly_variable_genes.krumsiek11-cell_ranger.h5ad test-data/pp.log1p.krumsiek11.h5ad test-data/pp.normalize_total.krumsiek11.h5ad test-data/pp.pca.krumsiek11_chunk.h5ad test-data/pp.recipe_seurat.recipe_zheng17.h5ad test-data/pp.recipe_weinreb17.paul15_subsample.updated.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/tl.embedding_density.umap.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.rank_genes_groups.liblinear.krumsiek11.h5ad test-data/tl.score_genes.krumsiek11.h5ad test-data/tl.score_genes_cell_cycle.krumsiek11.h5ad |
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| diff -r c0a80a16560f -r 18262103fa61 README.md --- a/README.md Tue Aug 20 09:50:59 2024 +0000 +++ b/README.md Sat Sep 14 12:45:03 2024 +0000 |
| [ |
| @@ -25,6 +25,7 @@ `pp.highly_variable_genes` | Extract highly variable genes `pp.subsample` | Subsample to a fraction of the number of observations `pp.downsample_counts` | Downsample counts so that each cell has no more than target_counts + `pp.scrublet` | Predict doublets 3. Normalize (`normalize.xml`) @@ -34,14 +35,18 @@ `pp.recipe_zheng17` | Normalization and filtering as of [Zheng17] `pp.recipe_weinreb17` | Normalization and filtering as of [Weinreb17] `pp.recipe_seurat` | Normalization and filtering as of Seurat [Satija15] + `external.pp.magic` | Denoising using Markov Affinity-based Graph Imputation of Cells (MAGIC) API 4. Remove confounders (`remove_confounder.xml`) Methods | Description --- | --- `pp.regress_out` | Regress out unwanted sources of variation - `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors + <!-- `pp.mnn_correct` | Correct batch effects by matching mutual nearest neighbors --> `pp.combat` | ComBat function for batch effect correction + `external.pp.bbknn` | Batch effect removal with Batch balanced KNN (BBKNN) + `external.pp.harmony_integrate` | Integrate multiple single-cell experiments with Harmony + `external.pp.scanorama_integrate` | Integrate multiple single-cell experiments with Scanorama 5. Clustering, embedding and trajectory inference (`cluster_reduce_dimension.xml`) @@ -49,14 +54,14 @@ --- | --- `tl.louvain` | Cluster cells into subgroups `tl.leiden` | Cluster cells into subgroups - `tl.pca` | Principal component analysis - `pp.pca` | Principal component analysis (appears to be the same func...) + `pp.pca` | Principal component analysis `tl.diffmap` | Diffusion Maps `tl.tsne` | t-SNE `tl.umap` | Embed the neighborhood graph using UMAP `tl.draw_graph` | Force-directed graph drawing `tl.dpt` | Infer progression of cells through geodesic distance along the graph `tl.paga` | Mapping out the coarse-grained connectivity structures of complex manifolds + `tl.embedding_density` | Calculate the density of cells in an embedding (per condition) 6. Plot (`plot.xml`) @@ -66,18 +71,20 @@ --- | --- `pl.scatter` | Scatter plot along observations or variables axes `pl.heatmap` | Heatmap of the expression values of set of genes + `pl.tracksplot` | Tracks plot of the expression values per cell `pl.dotplot` | Makes a dot plot of the expression values `pl.violin` | Violin plot `pl.stacked_violin` | Stacked violin plots `pl.matrixplot` | Heatmap of the mean expression values per cluster `pl.clustermap` | Hierarchically-clustered heatmap - + 2. Preprocessing Methods | Description --- | --- `pl.highest_expr_genes` | Plot the fraction of counts assigned to each gene over all cells `pl.highly_variable_genes` | Plot dispersions versus means for genes + `pl.scrublet_score_distribution` | Histogram of doublet scores 3. PCA @@ -96,12 +103,13 @@ `pl.umap` | Scatter plot in UMAP basis `pl.diffmap` | Scatter plot in Diffusion Map basis `pl.draw_graph` | Scatter plot in graph-drawing basis + `pl.embedding_density` | Density of cells in an embedding (per condition) 5. Branching trajectories and pseudotime, clustering Methods | Description --- | --- - `pl.dpt_groups_pseudotime` | Plot groups and pseudotime + <!-- `pl.dpt_groups_pseudotime` | Plot groups and pseudotime --> `pl.dpt_timeseries` | Heatmap of pseudotime series `pl.paga` | Plot the abstracted graph through thresholding low-connectivity edges `pl.paga_compare` | Scatter and PAGA graph side-by-side @@ -113,3 +121,8 @@ --- | --- `pl.rank_genes_groups` | Plot ranking of genes using dotplot plot `pl.rank_genes_groups_violin` | Plot ranking of genes for all tested comparisons + `pl.rank_genes_groups_stacked_violin` | Plot ranking of genes as stacked violin plot + `pl.rank_genes_groups_heatmap` | Plot ranking of genes as heatmap plot + `pl.rank_genes_groups_dotplot` | Plot ranking of genes as dotplot plot + `pl.rank_genes_groups_matrixplot` | Plot ranking of genes as matrixplot plot + `pl.rank_genes_groups_tracksplot` | Plot ranking of genes as tracksplot plot |
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| diff -r c0a80a16560f -r 18262103fa61 inspect.xml --- a/inspect.xml Tue Aug 20 09:50:59 2024 +0000 +++ b/inspect.xml Sat Sep 14 12:45:03 2024 +0000 |
| [ |
| b'@@ -1,102 +1,121 @@\n-<tool id="scanpy_inspect" name="Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">\n- <description> with scanpy</description>\n+<tool id="scanpy_inspect" name="Scanpy Inspect and manipulate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <macros>\n <import>macros.xml</import>\n- <xml name="score_genes_params">\n- <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling" help=""/>\n- <param argument="random_state" type="integer" value="0" label="Random seed for sampling" help=""/>\n+ <xml name="params_score_genes">\n+ <param argument="n_bins" type="integer" value="25" label="Number of expression level bins for sampling"/>\n+ <param argument="random_state" type="integer" value="0" label="Random seed for sampling"/>\n <expand macro="param_use_raw"/>\n </xml>\n- <token name="@CMD_score_genes_inputs@"><![CDATA[\n+ <token name="@CMD_PARAMS_SCORE_GENES@"><![CDATA[\n n_bins=$method.n_bins,\n random_state=$method.random_state,\n use_raw=$method.use_raw,\n copy=False\n- ]]></token>\n+ ]]>\n+ </token>\n <xml name="corr_method">\n <param argument="corr_method" type="select" label="P-value correction method">\n- <option value="benjamini-hochberg">Benjamini-Hochberg</option>\n+ <option value="benjamini-hochberg" selected="true">Benjamini-Hochberg</option>\n <option value="bonferroni">Bonferroni</option>\n </param>\n </xml>\n <xml name="fit_intercept">\n- <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true"\n- label="Should a constant (a.k.a. bias or intercept) be added to the decision function?" help=""/>\n+ <param argument="fit_intercept" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should a constant (a.k.a. bias or intercept) be added to the decision function?"/>\n </xml>\n <xml name="max_iter">\n- <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge" help=""/>\n+ <param argument="max_iter" type="integer" min="0" value="100" label="Maximum number of iterations taken for the solvers to converge"/>\n </xml>\n <xml name="multi_class">\n- <param argument="multi_class" type="select" label="Multi class" help="">\n+ <param argument="multi_class" type="select" label="Multi class">\n+ <option value="auto" selected="true">auto: selects \xe2\x80\x98ovr\xe2\x80\x99 if the data is binary and otherwise selects \xe2\x80\x98multinomial\xe2\x80\x99</option>\n <option value="ovr">ovr: a binary problem is fit for each label</option>\n <option value="multinomial">multinomial: the multinomial loss fit across the entire probability distribution, even when the data is binary</option>\n- <option value="auto">auto: selects \xe2\x80\x98ovr\xe2\x80\x99 if the data is binary and otherwise selects \xe2\x80\x98multinomial\xe2\x80\x99</option>\n </param>\n </xml>\n <xml name="penalty">\n- <param argument="penalty" type="select" label="Norm used in the penalization" help="">\n+ <param argument="penalty" type="select" label="Norm used in the penalization">\n+ <option value="l2" selected="true">l2</option>\n <option value="l1">l1</option>\n- <option value="l2">l2</option>\n- <option value="customized">customized</option>\n- </param>\n- </xml>\n- <xml name="custom_penalty">\n- <param argument="pen" type="text" value="" label="Norm used in the penalization" help="">\n- <expand macro="sanitize_query" />\n+ <yield/>\n </param>\n '..b'ontents>\n+ <has_h5_keys keys="uns/log1p"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <!-- test 12 -->\n+ <test expect_num_outputs="2">\n+ <param name="adata" value="krumsiek11.h5ad"/>\n+ <conditional name="method">\n+ <param name="method" value="pp.scale"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true"/>\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.scale"/>\n+ <has_text_matching expression="zero_center=True"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="var/mean,var/std"/>\n+ </assert_contents>\n+ </output> </test>\n+\n+ <!-- test 13 -->\n+ <test expect_num_outputs="2">\n+ <param name="adata" value="krumsiek11.h5ad"/>\n+ <conditional name="method">\n+ <param name="method" value="pp.scale"/>\n+ <param name="max_value" value="10"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true"/>\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.scale"/>\n+ <has_text_matching expression="zero_center=True"/>\n+ <has_text_matching expression="max_value=10.0"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="var/mean,var/std"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <!-- test 14 -->\n+ <test expect_num_outputs="2">\n+ <param name="adata" value="random-randint.h5ad"/>\n+ <conditional name="method">\n+ <param name="method" value="pp.sqrt"/>\n+ </conditional>\n+ <section name="advanced_common">\n+ <param name="show_log" value="true"/>\n+ </section>\n+ <output name="hidden_output">\n+ <assert_contents>\n+ <has_text_matching expression="sc.pp.sqrt"/>\n+ <has_text_matching expression="stats before sqrt: min= 0.0 max= 999.0 mean= 499.83777"/>\n+ <has_text_matching expression="stats after sqrt: min= 0.0 max= 31.606962 mean= 21.079018"/>\n+ </assert_contents>\n+ </output>\n+ <output name="anndata_out" ftype="h5ad">\n+ <assert_contents>\n+ <has_h5_keys keys="obs/index"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n Calculate quality control metrics., using `pp.calculate_qc_metrics`\n ===================================================================\n \n-Calculates a number of qc metrics for an AnnData object, largely based on calculateQCMetrics from scater. \n+Calculates a number of qc metrics for an AnnData object, largely based on calculateQCMetrics from scater.\n Currently is most efficient on a sparse CSR or dense matrix.\n \n It updates the observation level metrics with\n@@ -983,6 +1067,8 @@\n \n Marker gene overlap scores can be quoted as overlap counts, overlap coefficients, or jaccard indices. The method returns a pandas dataframe which can be used to annotate clusters based on marker gene overlaps.\n \n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.marker_gene_overlap.html>`__\n \n Logarithmize the data matrix (`pp.log1p`)\n =========================================\n' |
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| diff -r c0a80a16560f -r 18262103fa61 macros.xml --- a/macros.xml Tue Aug 20 09:50:59 2024 +0000 +++ b/macros.xml Sat Sep 14 12:45:03 2024 +0000 |
| [ |
| b'@@ -1,17 +1,15 @@\n <macros>\n- <token name="@TOOL_VERSION@">1.9.6</token>\n- <token name="@VERSION_SUFFIX@">4</token>\n- <token name="@profile@">21.09</token>\n+ <token name="@TOOL_VERSION@">1.10.2</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">21.09</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>\n- <requirement type="package" version="3.0.6">loompy</requirement>\n- <requirement type="package" version="0.10.1">leidenalg</requirement>\n- <requirement type="package" version="0.8.1">louvain</requirement>\n- <requirement type="package" version="1.5.3">pandas</requirement>\n- <requirement type="package" version="3.7">matplotlib</requirement>\n- <requirement type="package" version="0.12.2">seaborn</requirement>\n- <requirement type="package" version="3.0.0">magic-impute</requirement>\n+ <requirement type="package" version="0.10.3">anndata</requirement>\n+ <requirement type="package" version="1.26.4">numpy</requirement>\n+ <requirement type="package" version="2.2.2">pandas</requirement>\n+ <requirement type="package" version="1.14.1">scipy</requirement>\n+ <requirement type="package" version="0.14.2">statsmodels</requirement> \n <yield />\n </requirements>\n </xml>\n@@ -22,7 +20,7 @@\n </xml>\n <xml name="creators">\n <creator>\n- <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />\n+ <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/"/>\n </creator>\n </xml>\n <xml name="citations">\n@@ -31,28 +29,13 @@\n <citation type="doi">10.1093/gigascience/giaa102</citation>\n </citations>\n </xml>\n- <xml name="version_command">\n- <version_command><![CDATA[python -c "import scanpy as sc;print(\'scanpy version: %s\' % sc.__version__)"]]></version_command>\n- </xml>\n- <token name="@CMD@"><![CDATA[\n-cp \'$adata\' \'anndata.h5ad\' &&\n-cat \'$script_file\' > \'$hidden_output\' &&\n-python \'$script_file\' >> \'$hidden_output\' &&\n-ls . >> \'$hidden_output\' &&\n-touch \'anndata_info.txt\' &&\n-cat \'anndata_info.txt\' @CMD_prettify_stdout@\n- ]]>\n- </token>\n- <token name="@CMD_imports@"><![CDATA[\n-import scanpy as sc\n-import pandas as pd\n-import numpy as np\n- ]]>\n- </token>\n+ \n+ \n+ <!-- param macros -->\n <xml name="sanitize_query" token_validinitial="string.printable">\n <sanitizer>\n <valid initial="@VALIDINITIAL@">\n- <remove value="'" />\n+ <remove value="'"/>\n </valid>\n </sanitizer>\n </xml>\n@@ -62,58 +45,55 @@\n <add value=","/>\n </valid>\n </sanitizer>\n- </xml>\n+ </xml> \n <xml name="inputs_anndata">\n <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>\n </xml>\n- <token name="@CMD_read_inputs@"><![CDATA[\n-adata = sc.read_h5ad(\'anndata.h5ad\')\n-]]>\n- </token>\n <xml name="inputs_common_advanced">\n <section name="advanced_common" title="Advanced Options" expanded="false">\n- <param name="show_log" type="boolean" checked="false" label="Output Log?" />\n+ <param name="show_log" type="boolean" checked="false" label="Output Log?"/>\n </section>\n </xml>\n <xml name="anndata_outputs">\n- <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>\n- <data name="hidden_output" format="txt" label="Log file" >\n+ <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">\n+ <yield />\n+ </data>\n+ '..b'row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">\n <option value="muted">muted</option>\n <expand macro="seaborn_color_palette_options"/>\n </param>\n- <param argument="standard_scale" type="select" label="Standardize a dimension between 0 and 1" help="Each variable or observation is subtracted by the minimum and divided each by its maximum.">\n- <option value="None">No standardization</option>\n- <option value="var">Standardization on variable</option>\n- <option value="obs">Standardization on observation</option>\n- </param>\n- <expand macro="seaborn_violinplot"/>\n+ <expand macro="param_standard_scale"/>\n+ <expand macro="params_seaborn_violinplot"/>\n+ <param argument="yticklabels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Set to view the y tick labels"/>\n+ <expand macro="param_vmin" label="The value representing the lower limit of the color scale" help="Values smaller than vmin are plotted with the same color as vmin."/>\n+ <expand macro="param_vmax" label="The value representing the upper limit of the color scale" help="Values larger than vmax are plotted with the same color as vmax."/>\n+ <expand macro="param_vcenter"/>\n </xml>\n- <token name="@CMD_pl_stacked_violin@"><![CDATA[\n+ <token name="@CMD_PARAMS_PL_STACKED_VIOLIN@"><![CDATA[\n swap_axes=$method.swap_axes,\n- @CMD_conditional_stripplot@\n- scale=\'$method.violin_plot.scale\',\n- #if $method.row_palette\n+ @CMD_CONDITIONAL_STRIPPLOT@\n+ density_norm=\'$method.violin_plot.density_norm\',\n+ #if $method.row_palette:\n row_palette=\'$method.row_palette\',\n #end if\n- #if str($method.standard_scale) != \'None\'\n- standard_scale=\'$method.standard_scale\',\n+ @CMD_STANDARD_SCALE@\n+ @CMD_PARAMS_SEABORN_VIOLINPLOT@\n+ yticklabels=$method.yticklabels,\n+ #if str($method.vmin) != \'\':\n+ vmin=$method.vmin,\n #end if\n- @CMD_params_seaborn_violinplot@\n+ #if str($method.vmax) != \'\':\n+ vmax=$method.vmax,\n+ #end if\n+ #if str($method.vcenter) != \'\':\n+ vcenter=$method.vcenter,\n+ #end if\n ]]>\n </token>\n+\n+ <xml name="params_scatter_outine">\n+ <param argument="add_outline" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Add a thin border around groups of dots" help="In some situations this can enhance the aesthetics of the resulting image"/>\n+ <param name="outline_color_border" type="select" optional="true" label="Border color around the scatter dot" help="Default: black">\n+ <expand macro="matplotlib_color"/>\n+ </param>\n+ <param name="outline_color_gap" type="select" optional="true" label="Gap color between the border color and the scatter dot" help="Default: white">\n+ <expand macro="matplotlib_color"/>\n+ </param>\n+ <param argument="outline_width_border" type="float" value="0.3" optional="true" label=" width of the border color as a fraction of the scatter dot size "/>\n+ <param argument="outline_width_gap" type="float" value="0.05" optional="true" label="The width of the gap color"/>\n+ </xml>\n+ <token name="@CMD_SCATTER_OUTINE@"><![CDATA[\n+ add_outline=$method.add_outline,\n+ #if $method.outline_color_border and $method.outline_color_gap:\n+ outline_color=($method.outline_color_border, $method.outline_color_gap),\n+ #end if\n+ outline_width=($method.outline_width_border, $method.outline_width_gap),\n+ ]]>\n+ </token>\n+\n+\n+ <!-- unused macros -->\n+ <!-- <xml name="param_right_margin">\n+ <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel"/>\n+ </xml>\n+ <xml name="param_left_margin">\n+ <param argument="left_margin" type="float" value="1" label="Width of the space left of each plotting panel"/>\n+ </xml> -->\n </macros>\n' |
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