Running UseGalaxy R Script locally, looking at command line arguments


I ran edgeR version 3.24.1 on UseGalaxy. I want to run the R script that the UseGalaxy version of the tool output, locally on R. Is there a way to know how the web interface outputs arguments into the command line to run the script? Specifically I’d like to know how factors and levels are formatted into the “factInput” argument.

factInput", “i”, 2, “character” -String containing factors if manually input

This bit of code:

else {
factors <- unlist(strsplit(opt$factInput, “|”, fixed=TRUE))
factorData <- list() for (fact in factors) {
newFact <- unlist(strsplit(fact, split="::"))
factorData <- rbind(factorData, newFact)
} # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,…

leads me to believe the argument is "-i FACT_NAME|LEVEL,LEVEL,LEVEL,LEVEL

Can anyone help me?


1 Like

Hello @bgoldh

On the EdgeR tool form, expand the section for “Output Options” to generate the information directly.