diff --git a/tools/plotting/histogram.py b/tools/plotting/histogram.py
index b9d89425fd7..c7a5d36f9e7 100644
--- a/tools/plotting/histogram.py
+++ b/tools/plotting/histogram.py
@@ -62,6 +62,7 @@ def main():
             r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks )
             if density:
                 r.lines( r.density( a ) )
+            r.dev_off()
         except exc:
             stop_err("Building histogram resulted in error: %s." %str( exc ))
     else:
@@ -70,5 +71,7 @@ def main():
     if skipped_lines > 0:
         print "..skipped %d invalid lines starting with line #%d.  Value '%s' is not numeric." % ( skipped_lines, first_invalid_line, invalid_value )
 
+    r.quit( save="no" )
+    
 if __name__ == "__main__":
     main()
diff --git a/tools/plotting/histogram.xml b/tools/plotting/histogram.xml
deleted file mode 100644
index 8e335a962f3..00000000000
--- a/tools/plotting/histogram.xml
+++ /dev/null
@@ -1,31 +0,0 @@
-<tool id="Histogram1" name="Histogram">
-  <description>for any numeric column</description>
-  <command interpreter="python">plotter.py $input $col $bins $out_file1 hist</command>
-  <inputs>
-    <!-- <display>on column $col of $input with $bins bins</display> -->
-    <param format="text" name="input" type="data" label="Select Query" />
-    <param name="col" size="4" type="integer" value="5" label="Column to plot" />
-    <param name="bins" size="4" type="integer" value="10" label="Number of bins" />
-  </inputs>
-  <outputs>
-    <data format="png" name="out_file1" />
-  </outputs>
-  <code file="plot_filter.py"/>
-  <help>
-This tool builds a simple histogram for a given data column using a specified number of bins:
-
------
-
-**Syntax**
-
-- **Column to plot** is an integer. The first column is **1**
-- **Number of bins** is an integer between 1 and 99
-
------
-
-**Example**
-
-.. image:: ../static/images/histogram.png
-
-</help>
-</tool>
diff --git a/tools/plotting/scatter.xml b/tools/plotting/scatter.xml
deleted file mode 100644
index 071384b251c..00000000000
--- a/tools/plotting/scatter.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<tool id="Scatterplot1" name="Scatterplot">
-  <description>for any numeric column</description>
-  <command interpreter="python">plotter.py $input $col $style $out_file1 scatter</command>
-  <inputs>
-<!--    <display>on column $col of $input show $style</display> -->
-    <param format="text" name="input" type="data" label="Select Query"/>
-    <param name="col" size="4" type="integer" value="5" label="Column to plot"/>
-    <param name="style" type="select" label="Plot style">
-      <option value="L">Lines</option>
-      <option value="P">Points</option>
-      <option value="LP">Lines&amp;Points</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="png" name="out_file1" />
-  </outputs>
-  <help>This tool creates a simple scatterplot for a selected Query
-
------
-
-**Syntax**
-
-- **Column to plot** is an integer. The first column is **1**
-
------
-
-**Example**
-
-.. image:: ../static/images/scatter.png
- 
-</help>
-</tool>
diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml
index d4780447a7e..29c468c5813 100644
--- a/tools/plotting/scatterplot.xml
+++ b/tools/plotting/scatterplot.xml
@@ -2,16 +2,12 @@
   <description>of two numeric columns</description>
   <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
   <inputs>
-    <page>
-      <param name="input" format="tabular" type="data" label="Dataset" help="Query missing? See TIP below"/>
-    </page>
-    <page>
-      <param name="col1" type="select" label="Column for x axis" dynamic_options="get_columns( input )" />
-      <param name="col2" type="select" label="Column for y axis" dynamic_options="get_columns( input )" />
-      <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
-      <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
-      <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
-    </page>
+    <param name="input" type="data" format="tabular" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
+    <param name="col1" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for x axis" />
+    <param name="col2" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for y axis" />
+    <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
+    <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
+    <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
   </inputs>
   <outputs>
     <data format="pdf" name="out_file1" />
@@ -55,5 +51,4 @@ This tool creates a simple scatter plot between two variables containing numeric
 .. image:: ../static/images/scatterplot.png
 
 </help>
-  <code file="scatterplot_code.py" />
 </tool>
diff --git a/tools/plotting/scatterplot_code.py b/tools/plotting/scatterplot_code.py
deleted file mode 100644
index a8797292612..00000000000
--- a/tools/plotting/scatterplot_code.py
+++ /dev/null
@@ -1,42 +0,0 @@
-
-def get_columns( input ):
-    columns = []
-    elems = []
-
-    for i, line in enumerate( file ( input.file_name ) ):
-        valid = True
-        if line and not line.startswith( '#' ): 
-            line = line.rstrip('\r\n')
-            elems = line.split( '\t' )
-    
-            """
-            Since this tool requires users to select only those columns
-            that contain numerical values, we'll restrict the column select
-            list appropriately.
-            """
-            if len(elems) > 0:
-                for col in range(1, input.metadata.columns+1):
-                    try:
-                        val = float(elems[col-1])
-                        valid = True
-                    except:
-                        val = elems[col-1]
-                        if val:
-                            if val.strip().lower() == "na":
-                                valid = True
-                            else:
-                                valid = False
-                        else:
-                            valid = False
-                    if valid:
-                        option = "c" + str(col)
-                        columns.append((option,str(col),False))
-            if len(columns) > 0:
-                """
-                We have our select list built, so we can break out of the outer most for loop
-                """
-                break 
-        if i == 30:
-            break # Hopefully we never get here...
-
-    return columns
\ No newline at end of file