| Previous changeset 1:fb2f1b8b0013 (2022-12-04) Next changeset 3:cc768b0f41cf (2024-11-07) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c |
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modified:
scran-normalize.R scran_normalize.xml test-data/logcounts_hclust.tsv test-data/logcounts_igraph.tsv |
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added:
test-data/counts.tsv test-data/logcounts.tsv |
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removed:
test-data/counts.tab test-data/logcounts.tab |
| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 scran-normalize.R --- 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) |
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| diff -r fb2f1b8b0013 -r 6864acb21714 scran_normalize.xml --- 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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| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/counts.tab --- a/test-data/counts.tab Sun Dec 04 01:01:01 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/counts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tsv Sun Dec 10 00:27:45 2023 +0000 |
| b |
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|
| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/logcounts.tab --- a/test-data/logcounts.tab Sun Dec 04 01:01:01 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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|
| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/logcounts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/logcounts.tsv Sun Dec 10 00:27:45 2023 +0000 |
| b |
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|
| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/logcounts_hclust.tsv --- a/test-data/logcounts_hclust.tsv Sun Dec 04 01:01:01 2022 +0000 +++ b/test-data/logcounts_hclust.tsv Sun Dec 10 00:27:45 2023 +0000 |
| b |
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| b |
| diff -r fb2f1b8b0013 -r 6864acb21714 test-data/logcounts_igraph.tsv --- a/test-data/logcounts_igraph.tsv Sun Dec 04 01:01:01 2022 +0000 +++ b/test-data/logcounts_igraph.tsv Sun Dec 10 00:27:45 2023 +0000 |
| b |
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