# HG changeset patch
# User iuc
# Date 1726050078 0
# Node ID 2622dd85416f5e3dd0ec232f8d344110bb68d184
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
diff -r 000000000000 -r 2622dd85416f macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 11 10:21:18 2024 +0000
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+ 5.0
+ 0
+ 23.0
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+ r-seurat
+ fit-sne
+ bioconductor-limma
+ bioconductor-mast
+ bioconductor-deseq2
+ r-svglite
+ r-metap
+ bioconductor-glmGamPoi
+ umap-learn
+ leidenalg
+ r-harmony
+ bioconductor-batchelor
+ numpy
+ pandas
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+ 10.1038/s41587-023-01767-y
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+ /dev/null | grep -v -i "WARNING: ")
+ ]]>
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+ ]
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+ $hidden_output &&
+Rscript '$script_file' >> $hidden_output
+ ]]>
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+ advanced_common['show_log']
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+ method['method'] != 'Inspect'
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+ method['method'] == 'FindVariableFeatures' or method['method'] == 'SCTransform'
+ method['output_topN']['output_topN'] == 'true'
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+ method['method'] == 'FindAllMarkers' or method['method'] == 'FindMarkers' or method['method'] == 'FindConservedMarkers'
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+ method['method'] == 'RunPCA' and method['print_pcs']['print_pcs'] == 'true'
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] != 'General'
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] == 'General'
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+ plot_format == 'png'
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+ plot_format == 'pdf'
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+ plot_format == 'svg'
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+ plot_format == 'jpeg'
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+ plot_format == 'tex'
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+ plot_format == 'tiff'
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+ plot_format == 'eps'
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+ ^[\w\-.]+$
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+ ^[A-Za-z_]+$
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+ ^[\w\-., ]+$
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+ ^[\w[:punct:]]+$
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+ ^[\w[:punct:]]+$
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diff -r 000000000000 -r 2622dd85416f plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/plot.xml Wed Sep 11 10:21:18 2024 +0000
@@ -0,0 +1,1263 @@
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+ - Plot cells, features and dimensions
+
+ macros.xml
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+ ^[\d:]+$
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+ `__
+
+FeatureScatter
+==============
+
+Create a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class.
+Pearson correlation between the two features is displayed above the plot.
+
+More details on the `seurat documentation
+`__
+
+CellScatter
+===========
+
+Creates a plot of scatter plot of features across two single cells. Pearson correlation between the two cells is displayed above the plot.
+
+More details on the `seurat documentation
+`__
+
+VariableFeaturePlot
+===================
+
+View selected variable features on a plot of variances.
+
+More details on the `seurat documentation
+`__
+
+VizDimLoadings
+==============
+
+Visualize top genes associated with reduction components - default reduction is PCA.
+
+More details on the `seurat documentation
+`__
+
+DimPlot
+=======
+
+Graph the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique.
+By default, cells are colored by their identity class (can be changed with the group.by parameter).
+
+More details on the `seurat documentation
+`__
+
+DimHeatmap
+==========
+
+Draw a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores.
+Allows for nice visualization of sources of heterogeneity in the dataset.
+
+More details on the `seurat documentation
+`__
+
+ElbowPlot
+=========
+
+Plot the standard deviations of the principal components for easy identification of an elbow in the graph - plots PCA as default reduction.
+
+More details on the `seurat documentation
+`__
+
+FeaturePlot
+===========
+
+Color single cells on a dimensional reduction plot according to a 'feature' (i.e. gene expression, PC scores, number of genes detected, etc.)
+
+More details on the `seurat documentation
+`__
+
+DoHeatmap
+=========
+
+Draw a heatmap of single cell feature expression.
+
+More details on the `seurat documentation
+`__
+
+DotPlot
+=======
+
+Visualize how feature expression changes across different identity classes (e.g. clusters).
+The size of the dot encodes the percentage of cells within a class that express the gene, while the color encodes the AverageExpression level across all cells within a class.
+
+More details on the `seurat documentation
+`__
+
+ ]]>
+
+
\ No newline at end of file