This may not be the 'best' way, but it I've found it to be a workable
I'm running a Perl script that takes the tool-xml parameters, does some processing,
R to obtain a p-val calculation. The results are parsed and included in a formatted HTML
It's all code based.
You can likely use something similar in a Python script:
# --- create the R command
echo 'phyper($match, $listcount, $all, $qrycount, lower.tail = FALSE, log.p =
FALSE)' > rcmd
# --- run R in command line mode
R --slave -f rcmd > rpval
# --- open and parse results
open my $fh, "<", "rpval";
my $line = <$fh>;
$line =~ /\[1\] (.+)/;
hope you find this of use.
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