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$shellstring = '-v -in src_alignment.fasta ';
foreach my $key (keys(%{$param})) {
   CASE: {
...
      if ($key eq 'cg')          { $shellstring .= '-cg ';            
+                    last CASE; }
   }
}

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";
...
   }
   last CASE;
}