#echo "1: " $1 
#echo "2: " $2 
#echo "3: " $3 
#echo "4: " $4 
#echo "5: " $5 
#echo "6: " $6 
#echo "7: " $7 
#echo "8: " $8 
#echo "9: " $9 
#echo "10: " ${10} 
#echo "11: " ${11}  
#echo "12: " ${12} 
#echo "13: " ${13} 
#echo "14: " ${14}  
#echo "15: " ${15}  
#echo "16: " ${16}  
#echo "17: " ${17}  
#echo "18: " ${18} 
#echo "19: " ${19} 
#echo "20: " ${20} 
#echo "21: " ${21} 
#echo "22: " ${22} 
#echo "23: " ${23} 
#echo "23: " ${24} 
#echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18} ${19} ${20} ${21} ${22} ${23}

#get tool data and tool install directories
tooldir=$(cut -d';' -f1 <<< ${12})
tooldata=$(cut -d';' -f2 <<< ${12})

#create temp directory for row and col order and dendro files.
tdir=$tooldata/$(date +%y%m%d%M%S)
echo $tdir
mkdir $tdir
#run R to cluster matrix
output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
rc=$?;
if [ $rc != 0 ]
then
  echo $output;
  if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
  then
    echo "";
    echo "Note: This error can occur when there is no variation in a row or column.  Try a different distance measure or remove rows/columns without variation.";
    echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
  fi
  exit $rc;
fi
 
#there are a variable number of triplicate parameters for classification bars
count=0
classifications=''

#if row cut was done, add that autogenerated classification
if [ ${13} -gt 1 ]
then
  classifications="Class $tdir/ROfile.txt.cut row_categorical color_plot"
fi

#if col cut was done, add that autogenerated classification
if [ ${14} -gt 1 ]
then
  classifications="$classifications Class $tdir/COfile.txt.cut col_categorical  color_plot"
fi

#now add the user provided classification files 
for i in "$@"; do
  if [ $count -gt 20 ]
  then
#    echo "class entry: " $i
    classifications=$classifications' '$i
  fi
  count=$((count+1))
done
#echo "classifications: " $classifications

#call java program to generate NGCHM viewer files.
java -jar $tooldir/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt "${17}" "${19}" $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt "${18}" "${20}" ${11} "${21}" $classifications  
#clean up tempdir
rm -rf $tdir