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changeset 6:1f13d304ddbd draft

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Uploaded
author insilico-bob
date Thu, 20 Jun 2019 11:36:53 -0400
parents 15c71ed09efa
children c5489978071a
files CHM_Advanced.R GalaxyMapGen.jar heatmap_advanced.sh mda_advanced_heatmap_gen.xml mda_heatmap_viz.zip
diffstat 5 files changed, 539 insertions(+), 127 deletions(-) [+]
line wrap: on
line diff
--- a/CHM_Advanced.R	Thu Nov 08 14:59:57 2018 -0500
+++ b/CHM_Advanced.R	Thu Jun 20 11:36:53 2019 -0400
@@ -17,7 +17,7 @@
 
 performDataOrdering<-function(dataFile, rowOrderMethod, rowDistanceMeasure, rowAgglomerationMethod, colOrderMethod, colDistanceMeasure, colAgglomerationMethod,rowOrderFile, colOrderFile, rowDendroFile, colDendroFile, rowCut, colCut)
 { 
-   dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?"))
+   dataMatrix = read.table(dataFile, header=TRUE, sep = "\t", check.names = FALSE, row.names = 1, as.is=TRUE, na.strings=c("NA","N/A","-","?"))
    rowOrder <-  createOrdering(dataMatrix, rowOrderMethod, "row", rowDistanceMeasure, rowAgglomerationMethod)  
    if (rowOrderMethod == "Hierarchical") {
       writeHCDataTSVs(rowOrder, rowDendroFile, rowOrderFile)
Binary file GalaxyMapGen.jar has changed
--- a/heatmap_advanced.sh	Thu Nov 08 14:59:57 2018 -0500
+++ b/heatmap_advanced.sh	Thu Jun 20 11:36:53 2019 -0400
@@ -1,39 +1,355 @@
-#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}
+#echo "1: " $1  " 2: " $2 " 3: " $3 " 4: " $4  " 5: " $5 " 6: " $6 " 7: " $7 " 8: " $8 " 9: " $9 " 10: " ${10} 
+#echo "11: " ${11} " 12: " ${12} 13: " ${13} 14: " ${14} " 15: " ${15} " 16: " ${16} " 17: " ${17} " 18: " ${18} " 19: " ${19} " 20: " ${20} 
+#echo "21: "${21}" 22: "${22}" 23: "${23}" 24: "${24}" 25: "${25}" 26: "${26}" 27: "${27}" 28: "${28}" 29: "${29}" 30: "${30}
 
-#get tool data and tool install directories
-tooldir=$(cut -d';' -f1 <<< ${12})
-tooldata=$(cut -d';' -f2 <<< ${12})
+#Count total number of parameters, dataLayer parameters, and classification parameters
+parmSize=0
+classSize=0
+dataLayerSize=0
+attribSize=0
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	parmSize=$((parmSize+1))
+	if [ $currParm = "classification" ]
+	then
+		classSize=$((classSize+1))
+  	fi
+	if [ $currParm = "matrix_files" ]
+	then
+		dataLayerSize=$((dataLayerSize+1))
+  	fi
+	if [ $currParm = "attribute" ]
+	then
+		attribSize=$((attribSize+1))
+  	fi
+done
 
+if [ $dataLayerSize -lt 1 ]
+then
+	noDataLayer="ERROR: No Heat Map Matrices provided.  Please add at least one Heat Map Matrix to your request and try again."
+   	echo $noDataLayer
+   	exit $noDataLayer
+fi
+
+#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)
-echo $tdir
 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" ] && [ $currParm != "attribute" ]
+		then
+			#Parse pipe-delimited parameter parameter
+			parmJson=$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 <<< $i)
+			rowDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$rowLabels'"],'
+			rowCutType=$(cut -d'|' -f16 <<< $i)
+			rowTopItemsJson=''
+			rowTopItems=$(cut -d'|' -f13 <<< $i)
+			if [ $rowTopItems != "None" ] && [ $rowTopItems != "" ]
+			then
+				rowTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": ['
+				rowTopItems=${rowTopItems//,/'","'}
+				rowTopItemsJson=$rowTopItemsJson'"'$rowTopItems'"],'
+			fi
+			rowCutsJson=''
+			if [ $rowCutType != "none" ]
+			then
+				cutValues=$(cut -d'|' -f15 <<< $i) 
+				if [ $cutValues != "None" ] && [ $cutValues != "0" ]
+				then
+					if [ $rowCutType = "treecuts" ]
+					then
+						rowCutsJson=$rowCutsJson'"tree_cuts": "'$cutValues'",' 
+						rowCutsJson=$rowCutsJson'"cut_width": "5",' 
+					fi
+					if [ $rowCutType = "positional" ]
+					then
+						rowCutErrorVal=0
+						[[ $cutValues != ?(-)+([0-9,]) ]] && rowCutErrorVal=$((rowCutErrorVal+1))
+						if [ $rowCutErrorVal -gt 0 ]
+						then
+	   						echo "GALAXY PARAMETER WARNING: Non-numeric values found for Row Fixed Gap Locations. Ignoring parameter value: "$cutValues
+						else
+							rowCutsJson=$rowCutsJson'"cut_locations": ['$cutValues'],' 
+							rowCutsJson=$rowCutsJson'"cut_width": "5",' 
+						fi
+					fi
+				fi
+			fi
+			rowConfigJson=$rowConfigJson$rowDataTypeJson$rowCutsJson$rowTopItemsJson
+			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 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},'
+	  	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 <<< $i)
+			colDataTypeJson='"'$(cut -d'|' -f10 <<< $i)'":["'$colLabels'"],'
+			colCutType=$(cut -d'|' -f16 <<< $i)
+			colTopItemsJson=''
+			colTopItems=$(cut -d'|' -f13 <<< $i)
+			if [ $colTopItems != "None" ] && [ $colTopItems != "" ]
+			then
+				colTopItemsJson='"'$(cut -d'|' -f12 <<< $i)'": ['
+				colTopItems=${colTopItems//,/'","'}
+				colTopItemsJson=$colTopItemsJson'"'$colTopItems'"],'
+			fi
+			colCutsJson=''
+			if [ $colCutType != "none" ]
+			then
+				cutValues=$(cut -d'|' -f15 <<< $i) 
+				if [ $cutValues != "None" ] && [ $cutValues != "0" ]
+				then
+					if [ $colCutType = "treecuts" ]
+					then
+						colCutsJson=$colCutsJson'"tree_cuts": "'$cutValues'",' 
+						colCutsJson=$colCutsJson'"cut_width": "5",' 
+					fi
+					if [ $colCutType = "positional" ]
+					then
+						colCutErrorVal=0
+						[[ $cutValues != ?(-)+([0-9,]) ]] && colCutErrorVal=$((colCutErrorVal+1))
+						if [ $colCutErrorVal -gt 0 ]
+						then
+	   						echo "GALAXY PARAMETER WARNING: Non-numeric values found for Column Fixed Gap Locations. Ignoring parameter value: "$cutValues
+						else
+							colCutsJson=$colCutsJson'"cut_locations": ['$cutValues'],' 
+							colCutsJson=$colCutsJson'"cut_width": "5",' 
+						fi
+					fi
+				fi
+			fi
+			colConfigJson=$colConfigJson$colDataTypeJson$colCutsJson$colTopItemsJson
+			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 <<< $i)'","'$(cut -d'|' -f17 <<< $i)'":"'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'":"'$(cut -d'|' -f20 <<< $i)'"},'
+	  	fi
+	 fi
+	 ctr=$((ctr+1))
+done
+
+#END: Construct JSON for all non-repeating parameters
+#echo "rowOrder: "$rowOrder
+#echo "rowDistance: "$rowDistance
+#echo "rowAgglomeration: "$rowAgglomeration
+#echo "rowCuts: "$rowCuts
+#echo "rowLabels: "$rowLabels
+#echo "ROW CONFIG JSON: "$rowConfigJson
+#echo "colOrder: "$colOrder
+#echo "colDistance: "$colDistance
+#echo "colAgglomeration: "$colAgglomeration
+#echo "colCuts: "$colCuts
+#echo "colLabels: "$colLabels
+#echo "COL CONFIG JSON: "$colConfigJson
+
+#BEGIN: Construct JSON for data layers
+matrixJson='"matrix_files": [ '
+inputMatrix=''
+dataLayerIter=0
+dataLayerNames=''
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	if [ $currParm = "matrix_files" ]
+	then
+		if [ $dataLayerIter -lt 1 ]		
+		then
+			inputMatrix=$(cut -d'|' -f3 <<< $i)
+		fi
+		currMatrixName=$(cut -d'|' -f5 <<< $i)
+		dataLayerIter=$((dataLayerIter+1))
+  		if [[ $dataLayerNames =~ $currMatrixName ]]
+		then
+   			currMatrixName=$currMatrixName$dataLayerIter
+		fi 
+  		dataLayerNames=$dataLayerNames$currMatrixName
+  		colorPref=$(cut -d'|' -f16 <<< $i)
+  		colorMapJson=''
+  		if [ $colorPref = "defined" ]
+		then
+			#validations to place leading zero on first breakpoint (if necessary)
+			b1=$(cut -d'|' -f20 <<< $i)
+			b1first=$(cut -d'.' -f1 <<< $b1)
+			if [ $b1first = "-" ]
+			then 
+				b1="-0."$(cut -d'.' -f2 <<< $b1)
+			fi
+			if [ "$b1first" = "" ]
+			then 
+				b1="0"$b1
+			fi
+			#validations to place leading zero on second breakpoint (if necessary)
+			b2=$(cut -d'|' -f21 <<< $i)
+			b2first=$(cut -d'.' -f1 <<< $b2)
+			if [ $b2first = "-" ]
+			then 
+				b2="-0."$(cut -d'.' -f2 <<< $b2)
+			fi
+			if [ "$b2first" = "" ]
+			then 
+				b2="0"$b2
+			fi
+			#validations to place leading zero on third breakpoint (if necessary)
+			b3=$(cut -d'|' -f22 <<< $i)
+			b3first=$(cut -d'.' -f1 <<< $b3)
+			if [ $b3first = "-" ]
+			then 
+				b3="-0."$(cut -d'.' -f2 <<< $b3)
+			fi
+			if [ "$b3first" = "" ]
+			then 
+				b3="0"$b3
+			fi
+			#validation to ensure that all entered breakpoints are numeric values
+			regExp='^[+-]?([0-9]+\.?|[0-9]*\.[0-9]+)$'
+		    if [[ $b1 =~ $regExp ]] && [[ $b2 =~ $regExp ]] && [[ $b3 =~ $regExp ]]
+		    then
+				colorMapJson=$colorMapJson'"color_map": {"colors": ["'$(cut -d'|' -f17 <<< $i)'","'$(cut -d'|' -f18 <<< $i)'","'$(cut -d'|' -f19 <<< $i)'"],'
+				colorMapJson=$colorMapJson'"thresholds": ['$b1','$b2','$b3'],'
+				colorMapJson=$colorMapJson'"missing":"'$(cut -d'|' -f23 <<< $i)'"},'
+		    else
+		        echo "GALAXY PARAMETER WARNING: Not all user-defined breakpoints are numbers. Defined breakpoints and colors will be ignored."
+		    fi
+		fi  		
+		#Parse pipe-delimited parameter parameter
+		matrixJson=$matrixJson' {'$colorMapJson'"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$currMatrixName'","'$(cut -d'|' -f6 <<< $i)'":"'$(cut -d'|' -f7 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f10 <<< $i)'":"'$(cut -d'|' -f11 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"}'
+		if [ $dataLayerIter -lt $dataLayerSize ]		
+		then
+			matrixJson=$matrixJson','
+		fi
+  	fi
+done
+matrixJson=$matrixJson"],"
+#END: Construct JSON for data layers
+#echo "DATA LAYER JSON: "$matrixJson
+#echo "INPUT MATRIX: "$inputMatrix
+
+#BEGIN: Construct JSON for attributes
+attribJson='"chm_attributes": [ '
+attribIter=0
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	if [ $currParm = "attribute" ]
+	then
+		attribIter=$((attribIter+1))
+		attribParam=$(cut -d'|' -f2 <<< $i)
+		#Parse pipe-delimited 2-part data layer parameter
+		attribJson=$attribJson' {"'$(cut -d':' -f1 <<< $attribParam)'":"'$(cut -d':' -f2 <<< $attribParam)'"}'
+		if [ $attribIter -lt $attribSize ]		
+		then
+			attribJson=$attribJson','
+		fi
+  	fi
+done
+attribJson=$attribJson'],'
+#END: Construct JSON for attributes
+#echo "ATTRIB JSON: "$attribJson
+
+#BEGIN: Construct JSON for classification files
+classJson='"classification_files": [ '
+colCutClass=''
+rowCutClass=''
+if [ $rowCuts -gt 1 ]
+then
+	rowCutClass='{"name": "Class", "path": "'$tdir'/ROfile.txt.cut","position": "row", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}'
+fi
+
+if [ $colCuts -gt 1 ]
+then
+	if [ $rowCuts -gt 1 ] 
+	then
+		rowCutClass=$rowCutClass','
+	fi
+	colCutClass='{"name": "Class", "path": "'$tdir'/COfile.txt.cut","position": "column", "color_map": {"type": "discrete"}, "bar_type": "color_plot"}'
+	if [ $classSize -gt 0 ] 
+	then
+		colCutClass=$colCutClass','
+	fi
+else
+	if [ $rowCuts -gt 1 ] && [ $classSize -gt 0 ] 
+	then
+		rowCutClass=$rowCutClass','
+	fi
+fi
+
+classJson=$classJson$rowCutClass$colCutClass
+classIter=0
+for i in "$@"; do
+	currParm=$(cut -d'|' -f1 <<< $i)
+	if [ $currParm = "classification" ]
+	then
+		classIter=$((classIter+1))
+		className=$(cut -d'|' -f3 <<< $i)
+		#Parse pipe-delimited 3-part classification bar parameter
+		classJson=$classJson' {"'$(cut -d'|' -f2 <<< $i)'":"'$(cut -d'|' -f3 <<< $i)'","'$(cut -d'|' -f4 <<< $i)'":"'$(cut -d'|' -f5 <<< $i)'","'$(cut -d'|' -f8 <<< $i)'":"'$(cut -d'|' -f9 <<< $i)'","'$(cut -d'|' -f12 <<< $i)'":"'$(cut -d'|' -f13 <<< $i)'","'$(cut -d'|' -f14 <<< $i)'":"'$(cut -d'|' -f15 <<< $i)'"'
+		classCat=$(cut -d'|' -f7 <<< $i)
+		classColorType=$(cut -d'_' -f2 <<< $classCat)
+		classJson=$classJson','
+		classHeight=$(cut -d'|' -f11 <<< $i)
+		heightErrorVal=0
+		[[ $classHeight != ?(-)+([0-9]) ]] && heightErrorVal=$((heightErrorVal+1))
+		if [ $heightErrorVal -gt 0 ]
+		then
+			echo 'GALAXY PARAMETER WARNING: Non-numeric values found for covariate bar ('$className') height.  Height value ignored and default of 15 used: '$classHeight
+		else
+			classJson=$classJson'"height": "'$classHeight'",' 
+		fi
+		classJson=$classJson' "position":"'$(cut -d'_' -f1 <<< $classCat)'","color_map": {"type":"'$classColorType'"}}'
+		if [ $classIter -lt $classSize ]		
+		then
+			classJson=$classJson','
+		fi
+  	fi
+done
+classJson=$classJson']'
+#END: Construct JSON for classification files
+#echo "CLASSIFICATION JSON: "$classJson
+
+#Complete construction of Parameter JSON file by adding all JSON sections created above
+parmJson=$parmJson$rowConfigJson$colConfigJson$attribJson$matrixJson$classJson
+parmJson=$parmJson'}'
+#echo "COMPLETED PARAMETER JSON: "$parmJson
+
 #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} ${16} 2>&1)"
+output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"
+# Check for errors from R step, log them if found, and exit script
 rc=$?;
 if [ $rc != 0 ]
 then
@@ -41,40 +357,13 @@
   if [ `echo "$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.";
+    echo "NOTE 1: This error can occur when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
+    echo "NOTE 2: This error can occur when there is no variation in a data rows or columns in the input matrix.  Try a different distance measure or remove rows/columns without variation.";
   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  
+#Call java program to generate NGCHM viewer files.
+java -jar $tooldir/GalaxyMapGen.jar "$parmJson"
 #clean up tempdir
 rm -rf $tdir
--- a/mda_advanced_heatmap_gen.xml	Thu Nov 08 14:59:57 2018 -0500
+++ b/mda_advanced_heatmap_gen.xml	Thu Jun 20 11:36:53 2019 -0400
@@ -2,30 +2,76 @@
 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
   <requirements>
        <requirement type="package" version="3.4.1">r-base</requirement> 
-	   <requirement type="package" version="8">openjdk</requirement>
+		<requirement type="package" version="8.0.144">openjdk</requirement>
   </requirements>
   <description> Create Clustered Heat Maps with Advanced Options</description>
-<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh  'advanced' 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' 
-
-    "
+<command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh  "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth"
+	"row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}"      
+	"col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}"    
     #for $attr in $hm_attribute
-      '${attr.attrbute_key}':'${attr.attrbute_value}';
+      'attribute|${attr.attrbute_key}':'${attr.attrbute_value}'
     #end for
-    "
-
+    #for $mx in $matrices
+	   'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}'
+    #end for
     #for $op in $operations
-       '${op.class_name}'
-       '${op.repeatinput.file_name}'
-       '${op.cattype.cat}'
-       '${op.cattype.bartype}'
-      #end for
- 	'$output' 
+       'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}'
+    #end for
+ 	'output_location|$output' 
  </command>
 	<stdio>
       <exit_code range="1:" level="fatal" />
 	</stdio>
   <inputs>
-    <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>
+    <repeat name="matrices" title="Heat Map Matrices">
+    	<param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>
+    	<param name="dataLayerName" size="40" type="text" value="Data_Layer_name"  label="Data Layer Name" help="Name for data layer (no spaces).">
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
+        </param>   
+	    <param name="summarymethod" type="select"  label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view.">
+			<option value="average">Average</option>
+			<option value="sample">Sample</option>
+			<option value="mode">Mode</option>
+	    </param>
+  		<conditional name="colorsBreaks">
+			<param name="setColorsBreaks" type="select" label="Colors and Breakpoints" help="Select whether to set your own colors and breakpoints or use default values.">
+				<option value="none">Use System Generated Colors and Breakpoints</option>
+				<option value="defined">Define Your Own Colors and Breakpoints</option>	    
+			</param>
+	       	<when value="none">
+	 		    	<param name="matrixColor1" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak1" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixColor2" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak2" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixColor3" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="matrixBreak3" type="text" size="0" hidden="true" value="0"/>
+	 		    	<param name="missingColor" type="text" size="0" hidden="true" value="0"/>
+	       	</when>
+	       	<when value="defined">
+ 					<param name="matrixColor1" type="color" label="Color for Breakpoint One" value="#ff0000"/>
+ 					<param name="matrixBreak1" type="text" label="Value for Breakpoint One" value="-1"/>
+ 					<param name="matrixColor2" type="color" label="Color for Breakpoint Two" value="#ffffff"/>
+ 					<param name="matrixBreak2" type="text" label="Value for Breakpoint Two" value="0"/>
+ 					<param name="matrixColor3" type="color" label="Color for Breakpoint Three" value="#0000ff"/>
+ 					<param name="matrixBreak3" type="text" label="Value for Breakpoint Three" value="1"/>
+ 					<param name="missingColor" type="color" label="Color for Missing Values" value="#000000"/> 
+	        </when>
+        </conditional>
+	   	<param name="dataLayerSelectionColor" type="color" label="Color for selection box" value="#00ff38"/>
+   		<param name="dataLayerCutsColor" type="color" label="Color for Heat Map Gaps" value="#ffffff"/>
+   		<param name="dataLayerGridColor" type="color" label="Color for Heat Map Grid" value="#ffffff"/>
+	    <param name="dataLayerGridShow" type="select"  label="Show Heat Map Grid">
+			<option value="Y">Yes</option>
+			<option value="N">No</option>
+	    </param>
+    </repeat>
     <param name="hmname" size="40" type="text" value="Heat_Map_name"  label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
            <sanitizer>
               <valid>
@@ -44,10 +90,16 @@
                 <remove value=" "/> 
               </valid>
            </sanitizer>
-    <param name="summarymethod" 	type="select"  label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view.">
-		<option value="average">Average</option>
-		<option value="sample">Sample</option>
-		<option value="mode">Mode</option>
+    <param name="summaryDisplayWidth" 	type="select"  label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">
+		<option value="50">50%</option>
+		<option value="10">10%</option>
+		<option value="20">20%</option>
+		<option value="30">30%</option>
+		<option value="40">40%</option>
+		<option value="60">60%</option>
+		<option value="70">70%</option>
+		<option value="80">80%</option>
+		<option value="90">90%</option>
     </param>
       <conditional name="d_rows">
 			<param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is.">
@@ -58,12 +110,12 @@
 	        <when value="Hierarchical">
 				<param name="rowDistanceMeasure" type="select"  label="Row Distance Metric" help="For clustering, select the method of determining distance between rows.">
 					<option value="euclidean">Euclidean</option>
-					<option value="binary">Binary</option>
+					<!-- <option value="binary">Binary</option> ** breaks dendrogram -->
 					<option value="manhattan">Manhattan</option>
 					<option value="maximum">Maximum</option>
-					<option value="canberra">Canberra</option>	    
+					<!-- <option value="canberra">Canberra</option>	     ** breaks dendrogram  -->
 					<option value="minkowski">Minkowski</option>	    
-					<option value="correlation">Correlation</option>	    
+					<!-- <option value="correlation">Correlation</option>  ** breaks dendrogram	 -->    
 				</param>
 				<param name="rowAgglomerationMethod" type="select"  label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
 					<option value="average">Average Linkage</option>
@@ -71,9 +123,22 @@
 					<option value="single">Single Linkage</option>
 					<option value="ward" selected="true">Ward</option>
 					<option value="mcquitty">Mcquitty</option>	    
-					<option value="median">Median</option>	    
-					<option value="centroid">Centroid</option>	    
+					<!-- <option value="median">Median</option> ** breaks dendrogram	    
+					<option value="centroid">Centroid</option>	** breaks dendrogram -->    
 				</param>
+				<param name="rowDendroShow" type="select"  label="Show Row Dendrogram" help="For setting the visibility of the row dendrogram.">
+					<option value="ALL">Summary and Detail</option>
+					<option value="SUMMARY">Summary Only</option>
+					<option value="NONE">Hide</option>
+	    		</param>
+				<param name="rowDendroHeight" type="select"  label="Row Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
+					<option value="100">100%</option>
+					<option value="50">50%</option>
+					<option value="75">75%</option>
+					<option value="125">125%</option>
+					<option value="150">150%</option>
+					<option value="200">200%</option>
+	    		</param>
 	            <param name="rowDendroCut" type="select" label="Row Cluster Covariate Bar" help="To generate a row covariate bar based on clusters, select the number of clusters(classes) to use.">
 	        		<option value="0" selected="true" >None</option>
 	        		<option value="2" >2</option>
@@ -97,16 +162,16 @@
 		        	</when>
 		        	<when value="treecuts">
 			            <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." >
-			        		<option value="0t" selected="true" >None</option>
-			        		<option value="2t" >2</option>
-			        		<option value="3t" >3</option>
-			        		<option value="4t" >4</option>
-			        		<option value="5t" >5</option>
-			        		<option value="6t" >6</option>
-			        		<option value="7t" >7</option>
-			        		<option value="8t" >8</option>
-			        		<option value="9t" >9</option>
-			        		<option value="10t" >10</option>
+			        		<option value="0" selected="true" >None</option>
+			        		<option value="2" >2</option>
+			        		<option value="3" >3</option>
+			        		<option value="4" >4</option>
+			        		<option value="5" >5</option>
+			        		<option value="6" >6</option>
+			        		<option value="7" >7</option>
+			        		<option value="8" >8</option>
+			        		<option value="9" >9</option>
+			        		<option value="10" >10</option>
 			            </param>
 			        </when>
 		        	<when value="positional">
@@ -180,12 +245,12 @@
         <when value="Hierarchical">
 			<param name="columnDistanceMeasure" type="select"  label="Column Distance Metric" help="For clustering, select the method of determining distance between columns.">
 				<option value="euclidean">Euclidean</option>
-				<option value="binary">Binary</option>
+				<!-- <option value="binary">Binary</option> ** breaks dendrogram  -->
 				<option value="manhattan">Manhattan</option>
 				<option value="maximum">Maximum</option>
-				<option value="canberra">Canberra</option>	    
+				<!-- <option value="canberra">Canberra</option> ** breaks dendrogram  -->	    
 				<option value="minkowski">Minkowski</option>	    
-				<option value="correlation">Correlation</option>	    
+				<!-- <option value="correlation">Correlation</option>	** breaks dendrogram     -->
 			</param>
 			<param name="columnAgglomerationMethod" type="select"  label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
 				<option value="average">Average Linkage</option>
@@ -193,10 +258,23 @@
 				<option value="single">Single Linkage</option>
 				<option value="ward" selected="true">Ward</option>
 				<option value="mcquitty">Mcquitty</option>	    
-				<option value="median">Median</option>	    
-				<option value="centroid">Centroid</option>	    
+				<!-- <option value="median">Median</option>	  ** breaks dendrogram  
+				<option value="centroid">Centroid</option>	** breaks dendrogram     -->
 			</param>
-            <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use.">
+			<param name="columnDendroShow" type="select"  label="Show Column Dendrogram" help="For setting the visibility of the column dendrogram.">
+					<option value="ALL">Summary and Detail</option>
+					<option value="SUMMARY">Summary Only</option>
+					<option value="NONE">Hide</option>
+    		</param>
+			<param name="columnDendroHeight" type="select"  label="Column Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
+					<option value="100">100%</option>
+					<option value="50">50%</option>
+					<option value="75">75%</option>
+					<option value="125">125%</option>
+					<option value="150">150%</option>
+					<option value="200">200%</option>
+    		</param>
+           <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use.">
         		<option value="0" selected="true" >None</option>
         		<option value="2" >2</option>
         		<option value="3" >3</option>
@@ -219,16 +297,16 @@
 	        	</when>
 	        	<when value="treecuts">
 		            <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters.">
-		        		<option value="0t" selected="true" >None</option>
-		        		<option value="2t" >2</option>
-		        		<option value="3t" >3</option>
-		        		<option value="4t" >4</option>
-		        		<option value="5t" >5</option>
-		        		<option value="6t" >6</option>
-		        		<option value="7t" >7</option>
-		        		<option value="8t" >8</option>
-		        		<option value="9t" >9</option>
-		        		<option value="10t" >10</option>
+		        		<option value="0" selected="true" >None</option>
+		        		<option value="2" >2</option>
+		        		<option value="3" >3</option>
+		        		<option value="4" >4</option>
+		        		<option value="5" >5</option>
+		        		<option value="6" >6</option>
+		        		<option value="7" >7</option>
+		        		<option value="8" >8</option>
+		        		<option value="9" >9</option>
+		        		<option value="10" >10</option>
 		            </param>
 		        </when>
 	        	<when value="positional">
@@ -305,32 +383,77 @@
            </sanitizer>
         </param>
         <param name="repeatinput" type="data" format="Tabular" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/>
+		<param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/>
         <conditional name="cattype">
 			<param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
-			  <option value="row_categorical" >Row Categorical</option>
+			  <option value="row_discrete" >Row Categorical</option>
 			  <option value="row_continuous" >Row Continuous</option>
-			  <option value="column_categorical" >Column Categorical</option>
+			  <option value="column_discrete" >Column Categorical</option>
 			  <option value="column_continuous" >Column Continuous</option>
 			</param>
 	        <when value="row_continuous">
-		 		<param name="bartype" type="select" label="Display Type">
-				  <option value="color_plot" >Standard</option>
-				  <option value="bar_plot" >Bar Plot</option>
-				  <option value="scatter_plot" >Scatter Plot</option>
-				</param>
+        		<conditional name="scatbar">
+			 		<param name="bartype" type="select" label="Display Type">
+					  <option value="color_plot" >Standard</option>
+					  <option value="bar_plot" >Bar Plot</option>
+					  <option value="scatter_plot" >Scatter Plot</option>
+					</param>
+	        		<when value="color_plot">
+ 						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+	        		</when>
+	        		<when value="bar_plot">
+ 						<param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
+	        		</when>
+	        		<when value="scatter_plot">
+ 						<param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
+	        		</when>
+	        	</conditional>
 	        </when>
 	        <when value="column_continuous">
-		 		<param name="bartype" type="select" label="Display Type">
-				  <option value="color_plot" >Standard</option>
-				  <option value="bar_plot" >Bar Plot</option>
-				  <option value="scatter_plot" >Scatter Plot</option>
-				</param>
+        		<conditional name="scatbar">
+			 		<param name="bartype" type="select" label="Display Type">
+					  <option value="color_plot" >Standard</option>
+					  <option value="bar_plot" >Bar Plot</option>
+					  <option value="scatter_plot" >Scatter Plot</option>
+					</param>
+	        		<when value="color_plot">
+ 						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+	        		</when>
+	        		<when value="bar_plot">
+ 						<param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
+	        		</when>
+	        		<when value="scatter_plot">
+ 						<param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
+ 						<param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
+	        		</when>
+	        	</conditional>
 	        </when>
-	        <when value="column_categorical">
-	 	 		<param name="bartype" type="text"  hidden="true" value="color_plot"/>
+	        <when value="column_discrete">
+         		<conditional name="scatbar">
+					<param name="bartype" type="select" hidden="true">
+					  <option value="color_plot" >Standard</option>
+					</param>
+ 	        		<when value="color_plot">
+						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+ 					</when>
+	        	</conditional>
 	        </when>
-	        <when value="row_categorical">
-	 	 		<param name="bartype" type="text"  hidden="true" value="color_plot"/>
+	        <when value="row_discrete">
+         		<conditional name="scatbar">
+					<param name="bartype" type="select" hidden="true">
+					  <option value="color_plot" >Standard</option>
+					</param>
+ 	        		<when value="color_plot">
+						<param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
+ 						<param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
+ 					</when>
+	        	</conditional>
 	        </when>
 	 	</conditional>
      </repeat>       
Binary file mda_heatmap_viz.zip has changed