use strict ; use warnings ;

print join ",", map { if (m/[,"]/) { s/(\A|"|\n|(?<!\n)\Z)/"$1/g } ; $_ }
               split /~/ while <DATA>;
__DATA__
col1~col2~col3~col4~col5
data11~data12~data13~data14~da,data15
data21~"data22"~d"ata"23~data24~da"ta"25
data31~data32~data33~data34~"data35"
data,data41~data42~data43~data44~data45
data51,data52,data,junk,specialchar,sometingdata53~data54~data55