diff --git a/tools/tertiary-analysis/sceasy/sceasy_convert.xml b/tools/tertiary-analysis/sceasy/sceasy_convert.xml index 2d44a6c8..e6f62caa 100644 --- a/tools/tertiary-analysis/sceasy/sceasy_convert.xml +++ b/tools/tertiary-analysis/sceasy/sceasy_convert.xml @@ -30,6 +30,10 @@ -e 'srt <- readRDS("input.rds")' -e 'sceasy::convertFormat(srt, outFile="output.h5ad", from="seurat", to="anndata", assay="${conversion.assay}", main_layer="${conversion.dtype}")' -e 'print(srt)' +#else if $conversion.direction == "anndata2seurat" + -e 'srt <- sceasy::convertFormat("input.h5ad", from="anndata", to="seurat", main_layer="${conversion.assay}")' + -e 'saveRDS(srt, "output.rds")' + -e 'print(srt)' #end if ]]> @@ -74,6 +78,14 @@ + + + + + + + + @@ -87,6 +99,9 @@ conversion['direction'].endswith('anndata') + + conversion['direction'].endswith('seurat') + @@ -105,7 +120,7 @@ Convert scRNA data object between formats `sceasy::convertFormat()` Support the following conversion: * Loom <-> SingleCellExperiment (full) * SingleCellExperiment -> AnnData (matrix, metadata, reducedDim) - * Seurat -> AnnData (matrix, metadata, reducedDim) + * Seurat <-> AnnData (matrix, metadata, reducedDim) @HELP@