directory=$1
extension=$2
#outputdir=$3 #is created
logdir=$4
if [ ! -d $logdir ]; then mkdir -p $logdir; fi 
logfile="sbml2mdl-runner.log"
scriptfile="sbml2mdl-runner.sh" 
#reset scriptfile
echo "">$scriptfile
#reset logfile, otherwise logs will be always appended
echo "running $0 $*">$logfile
sbml2mdlscript=`dirname $0`/sbml2mdl

for file in $directory/*$extension
do
    #echo "$file"
#replace xml extension to mdl, in output dir $3
	outputdir=$3/`basename $file $extension`
    outfilename=$outputdir/`basename $file $extension`.mdl
    #make directory for outfile if necessary
#    if [ ! -d $outputdir ]; then mkdir -p $outputdir; fi 
    #echo "$outfilename"
#replace xml extension to log, in log dir $4
    logfilename=$4/`basename $file $extension`.log
    #echo "$logfilename"
#log found and generated filenames
	echo "found: $file -> $outfilename $logfilename" >> $logfile
	echo "$sbml2mdlscript $file $outfilename >> $logfilename" >> $logfile
	    echo "$sbml2mdlscript $file $outfilename >> $logfilename" >> $scriptfile
#start sbml2mdl with given args (write own log)      
#    exec $sbml2mdlscript $file $outfilename >> $logfilename#only one started (the one has errors though)  
done
`chmod +x $scriptfile`
exec $scriptfile