# HG changeset patch
# User iuc
# Date 1726050086 0
# Node ID 50c5abeb08ba036bd28f5810f5bfdee94ee61b16
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
diff -r 000000000000 -r 50c5abeb08ba inspect_and_manipulate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect_and_manipulate.xml Wed Sep 11 10:21:26 2024 +0000
@@ -0,0 +1,755 @@
+
+ - Inspect and Manipulate
+
+ macros.xml
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+ `__
+
+Inspect
+=======
+
+General - basic information about the Seurat Object
+Features - list of features, select which assay to display features from if object contains multimodal data
+Cells - list of cell barcodes/ids, select layer to display cells for if object contains multiple layers
+Idents - list showing Ident for each cell
+Metadata - table of cell metadata
+Matrix - show the full matrix
+
+Manipulate
+==========
+
+Functions to add, change, or remove selected elements of a Seurat Object.
+
+Change Idents
+=============
+
+Change which annotation in your cell metadata is used as the Ident column.
+
+Rename Idents
+=============
+
+Rename the classes in the Ident column (e.g. to replace cluster numbers with cell types).
+
+You have the option to stash the original idents in a new column called 'old.ident' before renaming the classes in the Ident column.
+
+AddMetaData
+===========
+
+Merge
+=====
+
+Combine two Seurat Objects into a single Seurat Object.
+Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer.
+
+Subset
+======
+
+Subset a group of cells based on their ident or another grouping in your cell metadata.
+
+DietSeurat
+==========
+
+Keep only certain aspects of the Seurat object.
+Can be useful in functions that utilize merge as it reduces the amount of data in the merge
+
+More details on these essential commands can be found in the `seurat documentation
+`__
+
+AggregateExpression
+===================
+
+Returns summed counts ("pseudobulk") for each identity class.
+
+More details on the `seurat documentation
+`__
+
+
+DefaultAssay
+============
+
+Set the default assay for multimodal data.
+
+You can use the Inspect - General function to check which assay is currently active and which other assays are available.
+
+ ]]>
+
+
diff -r 000000000000 -r 50c5abeb08ba macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 11 10:21:26 2024 +0000
@@ -0,0 +1,437 @@
+
+ 5.0
+ 0
+ 23.0
+
+
+ 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
+
+
+
+
+ 10.1038/s41587-023-01767-y
+
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+ /dev/null | grep -v -i "WARNING: ")
+ ]]>
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+ ]
+
+ $hidden_output &&
+Rscript '$script_file' >> $hidden_output
+ ]]>
+
+
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+
+
+ advanced_common['show_log']
+
+
+
+
+ method['method'] != 'Inspect'
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+
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+
+ method['method'] == 'FindVariableFeatures' or method['method'] == 'SCTransform'
+ method['output_topN']['output_topN'] == 'true'
+
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+ method['method'] == 'FindAllMarkers' or method['method'] == 'FindMarkers' or method['method'] == 'FindConservedMarkers'
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+ method['method'] == 'RunPCA' and method['print_pcs']['print_pcs'] == 'true'
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] != 'General'
+
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] == 'General'
+
+
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+ plot_format == 'png'
+
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+ plot_format == 'pdf'
+
+
+ plot_format == 'svg'
+
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+ plot_format == 'jpeg'
+
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+ plot_format == 'tex'
+
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+ plot_format == 'tiff'
+
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+ plot_format == 'eps'
+
+
+
+
+
+
+ ^[\w\-.]+$
+
+
+ ^[A-Za-z_]+$
+
+
+ ^[\w\-., ]+$
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+ ^[\w[:punct:]]+$
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+ ^[\w[:punct:]]+$
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