Re: [galaxy-user] plugging R into galaxy

OK. I have made some tests this morning to figure this all out. Indeed, the problem with ">" is that it catches every single message R sends to STDOUT and not only object of your interest, so this is definitely not a reliable solution. Solution suggests by Alex worked perfectly well. I would suggest also to use the 'trailingOnly=TRUE' option within the commandArgs() call in the R script. That allows you to only care about the args given after the '--args' option. You can then forget how many previous options you have in your command line (--vanilla, --slave, -f or others...). First parameter useful to your R script would then be commandArgs(trailingOnly=T)[1] and so on.

There is just another little point that I would like to clarify. At the beginning my tests didn't work at all and I realize that I have to give the full path to the R script (in the command tag) to make it work.