changeset 1:94ee8160ace3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf"

--- a/dropletutils.xml	Tue Jun 04 17:19:16 2019 -0400
+++ b/dropletutils.xml	Mon Aug 26 05:06:15 2019 -0400
@@ -3,7 +3,7 @@
     <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
     <macros>
         <token name="@PACKAGE_VERSION@" >1.2.1</token>
-        <token name="@GALAXY_VERSION@" >1</token>
+        <token name="@GALAXY_VERSION@" >2</token>
         <token name="@TXIN@">tenx.input</token>
         <token name="@TXOUT@">tenx.output</token>
         <xml name="test_dirin" >
@@ -18,6 +18,7 @@
     <requirements>
         <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement>
         <requirement type="package" version="1.2_17" >r-matrix</requirement>
+        <requirement type="package" version="1.10.1" >bioconductor-scater</requirement>
     </requirements>
     <version_command><![CDATA[
     Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d'

--- a/scripts/dropletutils.Rscript	Tue Jun 04 17:19:16 2019 -0400
+++ b/scripts/dropletutils.Rscript	Mon Aug 26 05:06:15 2019 -0400
@@ -6,6 +6,7 @@
 
 suppressWarnings(suppressPackageStartupMessages(require(DropletUtils)))
 suppressWarnings(suppressPackageStartupMessages(require(Matrix)))
+suppressWarnings(suppressPackageStartupMessages(require(scater)))
 
 source(args[1])
 
@@ -34,8 +35,9 @@
 read10xFiles <- function(filein, typein){
     sce <- NULL
     if (typein == "tsv"){
-        dat <- read.table(filein, header = TRUE,  sep='\t', stringsAsFactors=FALSE, quote="", row.names=1)
-        sce <- SingleCellExperiment(assays = list(counts = as.matrix(dat)))
+        ## Exploding memory problems occured here
+        ## - solution is to use the readSparseCounts function from scater
+        sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein)))
     }
     else if (typein == "h5ad"){
         sce <- read10xCounts(filein, col.names=T, type="HDF5")   # use barcodes.tsv as column names
@@ -91,7 +93,7 @@
 doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){
     sce <- read10xFiles(files$infile, in.type)
 
-    dparams$m = as.matrix(counts(sce))
+    dparams$m = counts(sce)
     called <- do.call(defaultDrops, c(dparams))
     print(table(called))
         
@@ -106,7 +108,7 @@
     sce <- read10xFiles(files$infile, in.type)
 
     bparams$... <- NULL ## hack
-    bparams$m = as.matrix(counts(sce))
+    bparams$m = counts(sce)
 
     br.out <- do.call(barcodeRanks, c(bparams))