$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; }
   }
}


##</code><code>##

if ($key eq 'groups') {
   if ($param->{$key} =~ m/[^0-9\,\-\|]/) { # check for illegal characters in group-definition
      print "\n>>> Illegal characters in groups-definition '".$param->{$key}."'! Only 0-9 and , and - and | are allowed!\n";
      $error = 1;
   }
   last CASE;
}
if ($key eq 'gh') {
   if ($param->{$key} =~ m/[^0-9]/) {
      print "\n>>> Illegal characters in graph-height '".$param->{$key}."'! Only 0-9 are allowed!\n";
      $error = 1;
   }
   last CASE;
}