| Previous changeset 0:252eded61848 (2019-09-26) Next changeset 2:6864acb21714 (2023-12-10) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_scran_normalize commit e0357f07fdabee1ec6614aca6f7b51095111e0d5 |
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modified:
scran-normalize.R scran_normalize.xml |
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| diff -r 252eded61848 -r fb2f1b8b0013 scran-normalize.R --- a/scran-normalize.R Thu Sep 26 10:50:55 2019 -0400 +++ b/scran-normalize.R Sun Dec 04 01:01:01 2022 +0000 |
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| @@ -1,59 +1,65 @@ # load packages that are provided in the conda env -options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = FALSE, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) + } +) loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") warnings() library(optparse) library(scran) -#Arguments -option_list = list( +# Arguments +option_list <- list( make_option( c("-d", "--data"), default = NA, - type = 'character', + type = "character", help = "Input file that contains count values to transform" ), make_option( c("-s", "--sep"), - default = '\t', - type = 'character', + default = "\t", + type = "character", help = "File separator [default : '%default' ]" ), make_option( "--cluster", - default=FALSE, - action="store_true", - type = 'logical', + default = FALSE, + action = "store_true", + type = "logical", help = "Whether to calculate the size factor per cluster or on all cell" ), make_option( c("-m", "--method"), - default = 'hclust', - type = 'character', + default = "hclust", + type = "character", help = "The clustering method to use for grouping cells into cluster : hclust or igraph [default : '%default' ]" ), make_option( "--size", default = 100, - type = 'integer', + type = "integer", help = "Minimal number of cells in each cluster : hclust or igraph [default : '%default' ]" ), make_option( c("-o", "--out"), default = "res.tab", - type = 'character', + type = "character", help = "Output name [default : '%default' ]" ) ) -opt = parse_args(OptionParser(option_list = option_list), +opt <- parse_args(OptionParser(option_list = option_list), args = commandArgs(trailingOnly = TRUE)) -if (opt$sep == "tab") {opt$sep = "\t"} +if (opt$sep == "tab") { + opt$sep <- "\t" + } -data = read.table( +data <- read.table( opt$data, check.names = FALSE, header = TRUE, @@ -62,10 +68,9 @@ ) ## Import data as a SingleCellExperiment object -sce <- SingleCellExperiment(list(counts=as.matrix(data))) +sce <- SingleCellExperiment(list(counts = as.matrix(data))) - -if(opt$cluster){ +if (opt$cluster) { clusters <- quickCluster(sce, min.size = opt$size, method = opt$method) ## Compute sum factors @@ -78,14 +83,14 @@ sce <- normalize(sce) -logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits=5), check.names = F) +logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits = 5), check.names = FALSE) write.table( logcounts, opt$out, - col.names = T, - row.names = F, - quote = F, + col.names = TRUE, + row.names = FALSE, + quote = FALSE, sep = "\t" ) |
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| diff -r 252eded61848 -r fb2f1b8b0013 scran_normalize.xml --- a/scran_normalize.xml Thu Sep 26 10:50:55 2019 -0400 +++ b/scran_normalize.xml Sun Dec 04 01:01:01 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="scran_normalize" name="scran_normalize" version="0.2.0"> +<tool id="scran_normalize" name="scran_normalize" version="0.2.1"> <description>Normalize raw counts expression values using deconvolution size factors</description> <requirements> <requirement type="package" version="1.6.2">r-optparse</requirement> @@ -16,7 +16,7 @@ --method '$metacell.method' --size '$metacell.size' #end if - -o ${output} + -o '${output}' ]]></command> <inputs> <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/> @@ -92,16 +92,6 @@ </help> <citations> - <citation type="bibtex"> - @Article{, - author = {Aaron T. L. Lun and Davis J. McCarthy and John C. Marioni}, - title = {A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor}, - journal = {F1000Res.}, - year = {2016}, - volume = {5}, - pages = {2122}, - doi = {10.12688/f1000research.9501.2}, - } - </citation> + <citation type="doi">10.12688/f1000research.9501.2</citation> </citations> </tool> |