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Changeset 17:2dfb2227a16c (2024-09-14)

Previous changeset 16:1072ce66b426 (2024-08-20) Next changeset 18:0185bd174ea0 (2024-09-19)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb

added:
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

diff -r 1072ce66b426 -r 2dfb2227a16c README.md
--- a/README.md Tue Aug 20 09:53:51 2024 +0000
+++ b/README.md Sat Sep 14 12:44:20 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.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_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

diff -r 1072ce66b426 -r 2dfb2227a16c macros.xml
--- a/macros.xml Tue Aug 20 09:53:51 2024 +0000
+++ b/macros.xml Sat Sep 14 12:44:20 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+ \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+ \n+ \n </macros>\n'

diff -r 1072ce66b426 -r 2dfb2227a16c plot.xml
--- a/plot.xml Tue Aug 20 09:53:51 2024 +0000
+++ b/plot.xml Sat Sep 14 12:44:20 2024 +0000

[

b'@@ -1,10 +1,13 @@\n-<tool id="scanpy_plot" name="Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">\n- <description> with scanpy</description>\n+<tool id="scanpy_plot" name="Scanpy plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="bio_tools"/>\n- <expand macro="requirements"/>\n+ <expand macro="requirements">\n+ <requirement type="package" version="3.9.1">matplotlib</requirement>\n+ <requirement type="package" version="0.13.2">seaborn</requirement>\n+ <requirement type="package" version="0.11.6">python-igraph</requirement>\n+ </expand>\n <stdio>\n <regex match="... storing" source="stderr" level="warning"/>\n </stdio>\n@@ -14,18 +17,18 @@\n ]]></command>\n <configfiles>\n <configfile name="script_file"><![CDATA[\n-@CMD_imports@\n-@CMD_read_inputs@\n+@CMD_IMPORTS@\n+@CMD_READ_INPUTS@\n \n sc.settings.figdir = \'.\'\n \n-#if $method.method == \'pl.scatter\'\n+#if str($method.method) == \'pl.scatter\':\n \n-#if $method.type.type == \'xy\':\n+ #if str($method.type.type) == \'xy\':\n x_field=\'$method.type.x\'\n y_field=\'$method.type.y\'\n \n-#if $method.type.log:\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@@ -39,425 +42,462 @@\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+ #end if\n+ #end if\n \n sc.pl.scatter(\n- @CMD_param_plot_inputs@\n- #if $method.type.type == \'xy\':\n+ @CMD_PARAM_PLOT_INPUTS@\n+ #if str($method.type.type) == \'xy\':\n x=x_field,\n y=y_field,\n- #if $method.type.color\n+ #if str($method.type.color) != \'\':\n color=\'$method.type.color\',\n- #end if\n- #if str(\'$method.type.layers.use_layers\') == \'true\'\n+ #end if\n+ #if str(\'$method.type.layers.use_layers\') == \'true\':\n layers=(\'$method.type.layers.layer_x\', \'$method.type.layers.layer_y\', \'$method.type.layers.layer_color\'),\n- #end if\n- #else\n+ #end if\n+ #else if str($method.type.type) == \'basis\':\n basis=\'$method.type.basis\',\n- #if $method.type.color\n- #set $color = ([x.strip() for x in str($method.type.color).split(\',\')])\n+ #if str($method.type.color) != \'\':\n+ #set $color = ([x.strip() for x in str($method.type.color).split(\',\')])\n color=$color,\n- #end if\n+ #end if\n #end if\n use_raw=$method.use_raw,\n sort_order=$method.sort_order,\n- @CMD_params_groups@\n- @CMD_params_pl_components@\n+ @CMD_PARAM_GROUPS@\n+ @CMD_PARAM_PL_COMPONENTS@\n projection=\'$method.plot.projection\',\n+ #if str($method.plot.legend_loc) != \'\':\n legend_loc=\'$method.plot.legend_loc\',\n- #if $method.plot.palette\n+ #end if\n+ @CMD_PARAM_LEGEND_FONTSIZE@\n+ legend_fontweight=\'$method.plot.legend_fontweight\',\n+ #if $method.plot.color_map:\n+ color_map=\'$method.plot.color_map\',\n+ #end if \n+ #if $method.plot.palette:\n palette=[\'$method.plot.palette\'],\n #end if\n- #if $method.plot.color_map\n- color_map=\'$method.plot.color_map\',\n- #end if\n- @CMD_param_legend_fontsize@\n- legend_fontweight=\'$method.plot.legend_fontweight\',\n- @CMD_param_title@\n- @CMD_param_size@\n- frameon=$method.plot.frameon)\n+ frameon=$method.plot.frameon,\n+ @CMD_PARAM_SIZE@\n+ @CMD_PARAM_TITLE@\n+ @CMD_SHOW_NONE@)\n \n-#else if $method.method == \'pl.heatmap\'\n-@CMD_var_names_header_check@\n+#else if str($method.method) == \'pl.heatmap\':\n+@CMD_VAR_NAMES_HEADER_CHECK@\n sc.pl.heatmap(\n- @CMD_param_plot_inputs@\n- #if $method.gene_symbols\n- gene_symbols=\'$method.gene_symbols\',\n- #end if\n- @CMD_params_inputs@\n- @CMD_params_plots@\n- @CMD_pl_heatmap@)\n+ @CMD_PARAM_PLOT_INPUTS@\n+ @CMD_PARAMS_INPUTS@\n+ @CMD_PARAM_GENE_SYMBOLS@\n+ @CMD_'..b'details on the `scanpy documentation\n <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__\n \n-Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)\n-===========================================================================================================\n+Embeddings: Scatter plot in graph-drawing basis (`pl.draw_graph`)\n+=================================================================\n \n More details on the `scanpy documentation\n-<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.draw_graph.html>`__\n+\n+Embeddings: Plot the density of cells in an embedding (per condition) (`pl.embedding_density`)\n+==============================================================================================\n+\n+More details on the `scanpy documentation\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.embedding_density.html>`__\n+\n+.. This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed.\n+.. Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)\n+.. ===========================================================================================================\n+\n+.. More details on the `scanpy documentation\n+.. <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__\n \n Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)\n =====================================================================================================\n@@ -2533,11 +2430,11 @@\n More details on the `scanpy documentation\n <https://scanpy.readthedocs.io/en/stable/api/generated/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+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://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__\n+<https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n \n Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)\n ====================================================================================\n@@ -2545,17 +2442,19 @@\n More details on the `scanpy documentation\n <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.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://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.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://scanpy.readthedocs.io/en/stable/api/generated/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://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__\n- ]]></help>\n+ ]]>\n+ </help>\n <expand macro="citations"/>\n </tool>\n'

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