| Previous changeset 0:4cd9f0008d9c (2019-06-04) Next changeset 2:a8aa294401be (2019-09-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 40d4a92c62d75fe931baba8657cde006a26d84cf" |
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modified:
dropletutils.xml scripts/dropletutils.Rscript |
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| diff -r 4cd9f0008d9c -r cfe1e6c28d95 dropletutils.xml --- a/dropletutils.xml Tue Jun 04 17:19:52 2019 -0400 +++ b/dropletutils.xml Mon Aug 26 05:06:39 2019 -0400 |
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| @@ -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' |
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| diff -r 4cd9f0008d9c -r cfe1e6c28d95 scripts/dropletutils.Rscript --- a/scripts/dropletutils.Rscript Tue Jun 04 17:19:52 2019 -0400 +++ b/scripts/dropletutils.Rscript Mon Aug 26 05:06:39 2019 -0400 |
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| @@ -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)) |