# HG changeset patch
# User iuc
# Date 1726050051 0
# Node ID 4341b8ff2a46613a8e7f3bcbaf7e77d3b2a8db37
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
diff -r 000000000000 -r 4341b8ff2a46 integrate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/integrate.xml Wed Sep 11 10:20:51 2024 +0000
@@ -0,0 +1,356 @@
+
+ and manipulate layers
+
+ macros.xml
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+ `__
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+Integrate
+=========
+
+Multiple layers are integrated to enable them to be analysed together.
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+Available methods are: CCA, Harmony, JointPCA, RPCA, FastMNN and scVI.
+
+More details on the `seurat documentation
+`__
+
+JoinLayers
+==========
+
+Multiple layers (e.g. those created using the split function) can be joined together in a single layer. No integration is performed by this function.
+
+More details on the `seurat documentation
+`__
+
+PrepSCTFindMarkers
+==================
+
+Given a merged object with multiple SCT models, this function uses minimum of the median UMI (calculated using the raw UMI counts) of individual objects to reverse the individual SCT regression model using minimum of median UMI as the sequencing depth covariate.
+The counts slot of the SCT assay is replaced with recorrected counts and the data slot is replaced with log1p of recorrected counts.
+
+More details on the `seurat documentation
+`__
+
+ ]]>
+
+
\ No newline at end of file
diff -r 000000000000 -r 4341b8ff2a46 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 11 10:20:51 2024 +0000
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+
+ 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
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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' >> $hidden_output
+ ]]>
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+ advanced_common['show_log']
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+
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+ method['method'] != 'Inspect'
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+ method['method'] == 'FindVariableFeatures' or method['method'] == 'SCTransform'
+ method['output_topN']['output_topN'] == 'true'
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+ method['method'] == 'FindAllMarkers' or method['method'] == 'FindMarkers' or method['method'] == 'FindConservedMarkers'
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+ method['method'] == 'RunPCA' and method['print_pcs']['print_pcs'] == 'true'
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] != 'General'
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+ method['method'] == 'Inspect' and method['inspect']['inspect'] == 'General'
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+ plot_format == 'png'
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+ plot_format == 'pdf'
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+ plot_format == 'svg'
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+ plot_format == 'jpeg'
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+ plot_format == 'tex'
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+ plot_format == 'tiff'
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+ plot_format == 'eps'
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+
+
+
+
+
+ ^[\w\-.]+$
+
+
+ ^[A-Za-z_]+$
+
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+ ^[\w\-., ]+$
+
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+ ^[\w[:punct:]]+$
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+ ^[\w[:punct:]]+$
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