Mercurial > repos > artbio > gsc_scran_normalize
changeset 2:6864acb21714 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c
| author | artbio |
|---|---|
| date | Sun, 10 Dec 2023 00:27:45 +0000 |
| parents | fb2f1b8b0013 |
| children | cc768b0f41cf |
| files | scran-normalize.R scran_normalize.xml test-data/counts.tab test-data/counts.tsv test-data/logcounts.tab test-data/logcounts.tsv test-data/logcounts_hclust.tsv test-data/logcounts_igraph.tsv |
| diffstat | 8 files changed, 342 insertions(+), 355 deletions(-) [+] |
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--- a/scran-normalize.R Sun Dec 04 01:01:01 2022 +0000 +++ b/scran-normalize.R Sun Dec 10 00:27:45 2023 +0000 @@ -1,15 +1,15 @@ -# load packages that are provided in the conda env 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) +library(dynamicTreeCut) # Arguments option_list <- list( @@ -20,12 +20,6 @@ help = "Input file that contains count values to transform" ), make_option( - c("-s", "--sep"), - default = "\t", - type = "character", - help = "File separator [default : '%default' ]" - ), - make_option( "--cluster", default = FALSE, action = "store_true", @@ -53,18 +47,15 @@ ) opt <- parse_args(OptionParser(option_list = option_list), - args = commandArgs(trailingOnly = TRUE)) + args = commandArgs(trailingOnly = TRUE)) -if (opt$sep == "tab") { - opt$sep <- "\t" - } data <- read.table( opt$data, check.names = FALSE, header = TRUE, row.names = 1, - sep = opt$sep + sep = "\t" ) ## Import data as a SingleCellExperiment object @@ -81,7 +72,7 @@ sce <- computeSumFactors(sce) } -sce <- normalize(sce) +sce <- logNormCounts(sce) logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits = 5), check.names = FALSE)
--- a/scran_normalize.xml Sun Dec 04 01:01:01 2022 +0000 +++ b/scran_normalize.xml Sun Dec 10 00:27:45 2023 +0000 @@ -1,8 +1,9 @@ -<tool id="scran_normalize" name="scran_normalize" version="0.2.1"> +<tool id="scran_normalize" name="scran_normalize" version="1.28.1+galaxy0"> <description>Normalize raw counts expression values using deconvolution size factors</description> <requirements> - <requirement type="package" version="1.6.2">r-optparse</requirement> - <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement> + <requirement type="package" version="1.28.1">bioconductor-scran</requirement> + <requirement type="package" version="1.63_1">r-dynamictreecut</requirement> + <requirement type="package" version="1.7.3">r-optparse</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -10,7 +11,6 @@ <command detect_errors="exit_code"><![CDATA[ Rscript $__tool_directory__/scran-normalize.R --data '$input' - --sep '$input_sep' #if $metacell.cluster == "Yes": --cluster --method '$metacell.method' @@ -19,11 +19,7 @@ -o '${output}' ]]></command> <inputs> - <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/> - <param name="input_sep" type="select" label="Input column separator"> - <option value="tab" selected="true">Tabulation</option> - <option value=",">Comma</option> - </param> + <param name="input" type="data" format="tabular" label="Raw counts of expression data" help = "A tsv file that must have an header line"/> <conditional name="metacell"> <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details"> <option value="Yes">Yes</option> @@ -45,18 +41,18 @@ </outputs> <tests> <test> - <param name="input" value="counts.tab" ftype="tabular"/> - <output name="output" file="logcounts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> + <output name="output" file="logcounts.tsv" ftype="tabular"/> </test> <test> - <param name="input" value="counts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> <param name="cluster" value="Yes"/> <param name="method" value="igraph"/> <param name="size" value="25"/> <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/> </test> <test> - <param name="input" value="counts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> <param name="cluster" value="Yes"/> <param name="method" value="hclust"/> <param name="size" value="25"/>
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4.07764 3.63498 0 0 0 0 0 0 0 0 0 4.9168 0 0 0 0 0 0 0 0 0 3.52045 0 0 0 7.28981 9.71881 0 7.68932 8.24185 0 7.16411 3.21029 0 0 6.23345 0 5.69375 0 TMEM238 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -DIAPH2 0 0 0 7.14159 9.92441 0 0 0 0 0 0 8.99567 0 0 0 1.57524 0 0 0 0 0 0 0 0 7.19462 0 0 0 0 6.38336 0 0 0 0 0 4.8876 0 0 0 0 6.81416 0 0 0 0 0 3.41985 0 0 0 4.96413 0 0 0 0 0 0 0 0 0 4.06734 0 0 0 0 4.78529 0 0 0 0 0 0 0 0 4.6655 0 0 0 0 5.4551 2.33446 0 6.55835 +DIAPH2 0 0 0 9.05432 8.38316 0 0 0 0 0 0 8.975 0 0 0 2.82067 0 0 0 0 0 0 0 0 8.17494 0 0 0 0 7.11501 0 0 0 0 0 6.65768 0 0 0 0 8.17481 0 0 0 0 0 3.04055 0 0 0 5.09132 0 0 0 0 0 0 0 0 0 1.60957 0 0 0 0 3.25862 0 0 0 0 0 0 0 0 7.84145 0 0 0 0 6.48747 2.01312 0 4.26427 MIR4753 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SULT2B1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PRKACG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0