diff scripts/dropletutils.Rscript @ 5:d5e4b59d5331 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"

--- a/scripts/dropletutils.Rscript	Thu Dec 05 06:32:08 2019 +0000
+++ b/scripts/dropletutils.Rscript	Wed Jan 29 20:07:15 2020 +0000
@@ -34,7 +34,7 @@
     if (typeout == "tsv"){
         writeTSV(fileout, getCounts(object))
     }
-    else if (typeout == "h5ad"){
+    else if (typeout == "h5"){
         write10xCounts(fileout, getCounts(object),
                        type="HDF5",
                        gene.symbol=determineGeneIDs(object),
@@ -55,7 +55,7 @@
         ## - solution is to use the readSparseCounts function from scater
         sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein)))
     }
-    else if (typein == "h5ad"){
+    else if (typein == "h5"){
         sce <- read10xCounts(filein, col.names=T, type="HDF5")   # use barcodes.tsv as column names
     }
     else if (typein == "directory"){
@@ -69,7 +69,7 @@
 ## Methods
 
 
-doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5ad", fdr_threshold = 0.01){
+doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5", fdr_threshold = 0.01){
     sce <- read10xFiles(files$infile, in.type)
 
     eparams$... <- NULL ## hack
@@ -115,7 +115,7 @@
 }
 
 
-doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){
+doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5"){
     sce <- read10xFiles(files$infile, in.type)
 
     dparams$m = counts(sce)