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@