use warnings;
use strict;

my $str = q(cd / ; /path/to/R/R_latest --vanilla --args "fName='rGSDPlan';jobCode=682718;jobId=6827181;" < job682718.R > job_6827181.txt);
my $new;
my $out = 1;
for (split //, $str) {
    $out = ! $out if /"/;
    $new .= (/;/ and $out) ? '&&' :  $_;
}