--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.sh	Thu Jun 20 11:39:46 2019 -0400
@@ -0,0 +1,147 @@
+#echo "1: " $1" 2: " $2" 3: " $3" 4: "$4" 5: "$5 " 6: "$6 "7: "$7" 8: "$8 " 9: "$9" 10: "${10}" 11: "${11} "12: "${12} 
+#echo " 13: "${13}" 14: "${14}" 15: "${15}" 16: "${16} "17: "${17}" 18: "${18}" 19: "${19}" 20: "${20}" 21: "${21} " 22: "${22}" 23:" ${23} 
+
+#Count total number of parameters and classification parameters
+parmSize=0
+classSize=0
+matrixSize=0
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	parmSize=$((parmSize+1))
+	if [ $currParm = "classification" ]
+	then
+		classSize=$((classSize+1))
+  	fi
+done
+
+#Get tool data and tool install directories
+tooldir=$1
+tooldata=$2
+#create temp directory for row and col order and dendro files.
+tdir=$tooldata/$(date +%y%m%d%M%S)
+mkdir $tdir
+#echo "tdir: "$tdir
+
+#Extract parameters for row and column order and dendro files
+rowOrderFile=$tdir/ROfile.txt
+rowDendroFile=$tdir/RDfile.txt
+colOrderFile=$tdir/COfile.txt
+colDendroFile=$tdir/CDfile.txt
+rowOrderJson='"order_file": "'$rowOrderFile'",'
+rowDendroJson='"dendro_file": "'$rowDendroFile'",'
+colOrderJson='"order_file": "'$colOrderFile'",'
+colDendroJson='"dendro_file": "'$colDendroFile'",'
+
+#BEGIN: Construct JSON for all non-repeating parameters
+parmJson='{'
+rowConfigJson='"row_configuration": {'
+colConfigJson='"col_configuration": {'
+
+ctr=0
+for i in "$@"; do
+	if [ $ctr -gt 1 ]
+	then
+		currParm=$(cut -d'|' -f1 <<< $i)
+		if [ $currParm != "matrix_files" ] && [ $currParm != "row_configuration" ] && [ $currParm != "col_configuration" ] && [ $currParm != "classification" ]
+		then
+			#Parse pipe-delimited parameter parameter
+			parmJson=$parmJson' "'$(cut -d'|' -f1 <<< $i)'":"'$(cut -d'|' -f2 <<< $i)'",'
+	  	fi
+		if [ $currParm = "row_configuration" ]
+		then
+			rowOrder=$(cut -d'|' -f3 <<< $i)
+			rowDistance=$(cut -d'|' -f5 <<< $i)
+			rowAgglomeration=$(cut -d'|' -f7 <<< $i)
+			rowCuts=$(cut -d'|' -f9 <<< $i)
+			rowLabels=$(cut -d'|' -f11 <<< $i)
+			dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"]'
+			if [ $rowOrder = 'Hierarchical' ]
+			then
+				rowConfigJson=$rowConfigJson$rowOrderJson$rowDendroJson
+			fi
+			rowConfigJson=$rowConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
+	  	fi
+		if [ $currParm = "col_configuration" ]
+		then
+			colOrder=$(cut -d'|' -f3 <<< $i)
+			colDistance=$(cut -d'|' -f5 <<< $i)
+			colAgglomeration=$(cut -d'|' -f7 <<< $i)
+			colCuts=$(cut -d'|' -f9 <<< $i)
+			colLabels=$(cut -d'|' -f11 <<< $i)
+			dataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"]'
+			if [ $colOrder = 'Hierarchical' ]
+			then
+				colConfigJson=$colConfigJson$colOrderJson$colDendroJson
+			fi
+			colConfigJson=$colConfigJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'",'$dataTypeJson'},'
+	  	fi
+	 fi
+	 ctr=$((ctr+1))
+done
+#END: Construct JSON for all non-repeating parameters
+#echo "rowCuts: "$rowCuts
+#echo "colCuts: "$colCuts
+#echo "ROW CONFIG JSON: "$rowConfigJson
+#echo "COL CONFIG JSON: "$colConfigJson
+
+#BEGIN: Construct JSON for data layers
+matrixJson='"matrix_files": [ '
+inputMatrix=''
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	if [ $currParm = "matrix_files" ]
+	then
+		#Parse pipe-delimited parameter parameter
+		matrixJson=$matrixJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'"}'
+		inputMatrix=$(cut -d'|' -f3 <<< $i)
+  	fi
+done
+matrixJson=$matrixJson"],"
+#END: Construct JSON for data layers
+
+#BEGIN: Construct JSON for classification files
+classJson='"classification_files": [ '
+classIter=0
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	if [ $currParm = "classification" ]
+	then
+		classIter=$((classIter+1))
+		#Parse pipe-delimited 3-part classification bar parameter
+		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'"'
+		classCat=$(cut -d'|' -f7 <<< $i)
+		classColorType=$(cut -d'_' -f2 <<< $classCat)
+		classJson=$classJson','
+		classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
+		if [ $classIter -lt $classSize ]		
+		then
+			classJson=$classJson','
+		fi
+  	fi
+done
+classJson=$classJson']'
+#END: Construct JSON for classification files
+
+parmJson=$parmJson$matrixJson$rowConfigJson$colConfigJson$classJson
+parmJson=$parmJson'}'
+#echo "HEATMAP PARAMETERS JSON: "$parmJson	
+
+#run R to cluster matrix
+output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"
+rc=$?;
+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
+
+#call java program to generate NGCHM viewer files.
+java -jar $tooldir/GalaxyMapGen.jar "$parmJson"
+#clean up tempdir
+rm -rf $tdir