# HG changeset patch
# User iuc
# Date 1695290515 0
# Node ID a8305cf0c951511f95bebd6bacd6caf13c1ffe4f
# Parent f2843df56434b048ee56a885f47a2bb2ccecd8f2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
diff -r f2843df56434 -r a8305cf0c951 edger.R
--- a/edger.R Sat Dec 18 16:15:09 2021 +0000
+++ b/edger.R Thu Sep 21 10:01:55 2023 +0000
@@ -40,9 +40,9 @@
time_start <- as.character(Sys.time())
# setup R error handling to go to stderr
-options(show.error.messages = F, error = function() {
+options(show.error.messages = FALSE, error = function() {
cat(geterrmessage(), file = stderr())
- q("no", 1, F)
+ q("no", 1, FALSE)
})
# we need that to not crash galaxy with an UTF8 error on German LC settings.
@@ -105,8 +105,7 @@
} else if (substring(file, 1L, 1L) == "|") {
file <- pipe(substring(file, 2L), "w")
on.exit(close(file))
- }
- else {
+ } else {
file <- file(file, ifelse(append, "a", "w"))
on.exit(close(file))
}
@@ -181,7 +180,7 @@
opt <- getopt(spec)
-if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
+if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
cat("A counts matrix (or a set of counts files) is required.\n")
q(status = 1)
}
@@ -387,7 +386,7 @@
# Name rows of factors according to their sample
row.names(factors) <- names(data$counts)
-factor_list <- sapply(names(factors), paste_listname)
+factor_list <- names(factors)
# Generating the DGEList object "data"
samplenames <- colnames(data$counts)
@@ -405,7 +404,7 @@
}
formula <- formula(formula)
-design <- model.matrix(formula)
+design <- model.matrix(formula, factors)
for (i in seq_along(factor_list)) {
colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
diff -r f2843df56434 -r a8305cf0c951 edger.xml
--- a/edger.xml Sat Dec 18 16:15:09 2021 +0000
+++ b/edger.xml Thu Sep 21 10:01:55 2023 +0000
@@ -4,11 +4,8 @@
3.36.0
- 0
+ 1
-
- edger
-
topic_3308
@@ -16,7 +13,10 @@
operation_3563
operation_3223
-
+
+ edger
+ edger
+
bioconductor-edger
bioconductor-limma
@@ -26,11 +26,9 @@
r-scales
-
/dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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