No problem, here's the code generating $shellstring:

$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'}) { $shellstring .= '-sa '; } # '-ca' o
+verrides '-sa' 
         last CASE;
      }
      if ($key eq 'ca')          { $shellstring .= '-ca ';            
+                    last CASE; }
      if ($key eq 'cg')          { $shellstring .= '-cg ';            
+                    last CASE; }
   }
}
[download]

'src_alignment.fasta' is a file from upload or FORM data from a user, which will be mangled by the external script. '$param->{'groups'}' and '$param->{'gh'}' is tested in another subroutine for validity:

if ($key eq 'groups') {
   if ($param->{$key} =~ m/[^0-9\,\-\|]/) { # check for illegal charac
+ters in group-definition
      print "\n>>> Illegal characters in groups-definition '".$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;
}
[download]

If '$error' is found to be 1, the CGI-script exits and prints error messages. As I can see now from the anwers I got here my variables ('groups' and 'gh' especially) are not untainted "enough" or at all...just checking for validity is not enough here as far as I can see.

Thanks a lot for your help!