Following the discussion on this topic, the solution: You can run R 'straight' in galaxy without a wrapper: <command>R --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Rscript --args $infile $outfile</command> The input is never a big problem in galaxy, but how to capture the output was not so clear to me. So, Make sure your output file can be seen by galaxy (which was basically my problem): <inputs> <param name="infile" type="data" format="tabular"/> </inputs> <outputs> <data name="outfile" type="data" format="tabular"/> </outputs> And in R making sure, the output file has a name as well: write.table(data, sep="\t", file=out.file, row.names=F) Thanks for all the help!!