--- a/mda_advanced_heatmap_gen.xml	Tue Dec 05 14:59:26 2017 -0500
+++ b/mda_advanced_heatmap_gen.xml	Thu Feb 08 14:47:49 2018 -0500
@@ -1,8 +1,10 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.1.1">
-  <description> Create Clustered Heat Maps</description>
-<!-- command interpreter="python" detect_errors="aggressive">$__tool_directory__/mad_advanced_heatmap_gen.py  'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType  -->
-<command interpreter="bash" detect_errors="aggressive">$__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__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' 
+<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
+  <requirements>
+    <requirement type="package" version="3.4.1">r-base</requirement> 
+  </requirements>
+  <description> Create Clustered Heat Maps with Advanced Options</description>
+<command interpreter="bash" detect_errors="aggressive">$__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' 
 
     "
     #for $attr in $hm_attribute
@@ -23,8 +25,24 @@
 	</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."/>
-    <param name="hmname" size="20" type="text" value="Heat_Map_name"  label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
+    <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>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
+              </valid>
+           </sanitizer>
     <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/>
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <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>
@@ -275,17 +293,17 @@
         <option value="bio.protein.uniprot" >UniProt Id</option>
     </param>    
     <repeat name="operations" title="Covariate Bars">
-        <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map.">
-           <sanitizer invalid_char="_">
-              <valid initial="none">
-                <add preset="string.letters"/>
-                <add preset="string.digits"/>
+        <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
+           <sanitizer>
+              <valid>
+                <add preset="string.printable"/>
+            	<remove value="&quot;"/>
+            	<remove value="&apos;"/>
+                <remove value=" "/> 
               </valid>
-              <mapping initial="none">
-              </mapping>
            </sanitizer>
         </param>
-        <param name="repeatinput" type="data" format="text" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/>
+        <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."/>
         <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>