elsif($output eq "Inhouse") {
         
...

and here just implemente the counter. you can do the same thing for for previous decisions, if needed 
...
        
            else {
                $counter->{$save{$sam}{plateid}}++;
                print OUT "$counter->{$save{$sam}{plateid}},$save{$sam}{platename},$save{$sam}{well},$save{$sam}{case},$save{$sam}{plateid}_$save{$sam}{well}_$save{$sam}{clone},Homo sapiens,$save{$sam}{gender},,$save{$sam}{vol},50,$save{$sam}{extmethod},,0,$save{$sam}{father},$save{$sam}{mother},,$save{$sam}{source}\n";
            
            }
                
 ...