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) 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.
<command interpreter="bash"> r_script_wrapper.sh rcode.R --args $in_data $out_data </command> ### FAILURE
<command interpreter="bash"> r_script_wrapper.sh /full/path/to/rcode.R --args $in_data $out_data </command> ### SUCCESS
However, r_script_wrapper.sh and rcode.R are in the same directory.
To shed a light on this, I made an `echo $PWD` in r_script_wrapper.sh and it returned :
where Num is the number of the job submitted to the PBS queue.
Is that a known feature ?
here follows the content of r_script_wrapper.sh
# Function that writes a message to stderr and exits
echo "$@" >&2
# Ensure R executable is found
which R > /dev/null || fail "'R' is required by this tool but was not found on path"
# Extract first argument
# Ensure the file exists
test -f $rcode || fail "R input file '$rcode' does not exist"
# Invoke R
R --vanilla --slave --file=$rcode --args $*
On 11 November 2010 09:07, Freddy <firstname.lastname@example.org>
The out.data is simply picked up by galaxy:
As long as you define your variable capturing the output and also in your tool.xml file.
Make sure the output is defined as "data" in the tool.xml file.
Initially I thought the same thing, but the piping is not needed with '>', worse, it doesn't work like that.