$shellstring = '-v -in src_alignment.fasta ';
foreach my $key (keys(%{$param})) {
   CASE: {
      if ($key eq 'groups')      { $shellstring .= '-groups "'.$param->{'groups'}.'" ';   last CASE; }
      if ($key eq 'ngra')        { $shellstring .= '-ngra ';                              last CASE; }
      if ($key eq 'gh')          { $shellstring .= '-gh '.$param->{'gh'}.' ';             last CASE; }
      if ($key eq 'sa')          { 
         unless ($param->{'ca'}) { $shellstring .= '-sa '; } # '-ca' overrides '-sa' 
         last CASE;
      }
      if ($key eq 'ca')          { $shellstring .= '-ca ';                                last CASE; }
      if ($key eq 'cg')          { $shellstring .= '-cg ';                                last CASE; }
   }
}