diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index ad6785a8c66..b0aa334ecdc 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -241,9 +241,7 @@ def db_next_hid( self ):
 History._next_hid = db_next_hid
     
 def init( file_path, url, **kwargs ):
-    """
-    Connect mappings to the database
-    """
+    """Connect mappings to the database"""
     create_tables = kwargs.pop( 'create_tables', False )
     # Connect dataset to the file path
     Dataset.file_path = file_path
@@ -255,7 +253,7 @@ def init( file_path, url, **kwargs ):
             if table.columns.has_key( "update_time" ):
                 table.columns['update_time'].type = TIMESTAMP()
     # Connect the metadata to the database. 
-    if url.find( "sqlite" ) < 0 and url.find( '///' ) >= 0:
+    elif url.startswith( "postgresql:///" ):
         import psycopg
         try:
             dbconn = url.split('///')
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index 892308a17f5..3198e0d8ab3 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -2,7 +2,7 @@
   <description>data in ascending or descending order</description>
   <command interpreter="python">sorter.py -i $input -o $out_file1 -cols $column -order $order -style $style</command>
   <inputs>
-    <param format="tabular" name="input" type="data" label="Sort Query" refresh_on_change="True" />
+    <param format="tabular" name="input" type="data" label="Sort Query" />
     <param name="column" label="on column" type="columnlist" assoc_dataset="input" />
     <param name="order" type="select" label="in">
       <option value="ASC">Ascending order</option>
diff --git a/tools/filters/uniq.xml b/tools/filters/uniq.xml
index a0563b41969..8d3dd9d051b 100644
--- a/tools/filters/uniq.xml
+++ b/tools/filters/uniq.xml
@@ -2,7 +2,7 @@
   <description>occurences of each record</description>
   <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command>
   <inputs>
-    <param name="input" type="data" format="tabular" label="from query" refresh_on_change="True" help="Query missing? See TIP below"/>
+    <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/>
     <param name="column" type="columnlist" assoc_dataset="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
     <param name="delim" type="select" label="Delimited by">
       <option value="T">Tab</option>
diff --git a/tools/plotting/histogram.py b/tools/plotting/histogram.py
index 91baebd0265..f746cd5ce3c 100644
--- a/tools/plotting/histogram.py
+++ b/tools/plotting/histogram.py
@@ -36,10 +36,16 @@ def main():
         if line and not line.startswith( '#' ): 
             # Extract values and convert to floats
             row = []
-            fields = line.split( "\t" )
-            val = fields[column]
-            if val.lower() == "na":
-                row.append( float( "nan" ) )
+            try:
+                fields = line.split( "\t" )
+                val = fields[column]
+                if val.lower() == "na":
+                    row.append( float( "nan" ) )
+            except:
+                valid = False
+                skipped_lines += 1
+                if not first_invalid_line:
+                    first_invalid_line = i+1
             else:
                 try:
                     row.append( float( val ) )
diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram2.xml
index aca50c2eacc..02b7581dff1 100644
--- a/tools/plotting/histogram2.xml
+++ b/tools/plotting/histogram2.xml
@@ -2,7 +2,7 @@
   <description>of a numeric column</description>
   <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density</command>
   <inputs>
-    <param name="input" type="data" format="tabular" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
+    <param name="input" type="data" format="tabular" label="Dataset" help="Query missing? See TIP below"/>
     <param name="numerical_column" type="columnlist" assoc_dataset="input" numerical="True" label="Numerical column for x axis" />
     <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
     <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml
index 29c468c5813..57573a3f74c 100644
--- a/tools/plotting/scatterplot.xml
+++ b/tools/plotting/scatterplot.xml
@@ -2,7 +2,7 @@
   <description>of two numeric columns</description>
   <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
   <inputs>
-    <param name="input" type="data" format="tabular" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
+    <param name="input" type="data" format="tabular" label="Dataset" 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"/>
diff --git a/tools/stats/aggregate_scores_in_intervals.xml b/tools/stats/aggregate_scores_in_intervals.xml
deleted file mode 100644
index bdffbeba4ba..00000000000
--- a/tools/stats/aggregate_scores_in_intervals.xml
+++ /dev/null
@@ -1,60 +0,0 @@
-<tool id="aggregate_scores_in_intervals1" description="from the table browser (equivalent to wiggle format)." name="Aggregate datapoints">
-  <description>Appends the average, min, max, sum, and count of datapoints per interval</description>
-  <command interpreter="python2.4">aggregate_scores_in_intervals.py $input2 $input1 $input1_chromCol $input1_startCol $input1_endCol $out_file1</command>
-  <inputs>
-    <page>
-      <param format="wig" name="input2" type="data" label="Datapoints from table browser"/>
-      <param format="interval" name="input1" type="data" label="Interval file"/>
-    </page>
-  </inputs>
-  <outputs>
-    <data format="interval" name="out_file1" metadata_source="input2"/>
-  </outputs>
-  <!-- TODO: This tool is currently not being used, uncomment and correct the tests if it ever is...
-  <tests>
-    <test>
-      <param name="input1" value="aggregate_binned_scores_in_intervals.bed" />
-      <param name="datasets" value="aggregate_binned_scores_in_intervals.wig" />
-      <output name="out_file1" file="aggregate_binned_scores_in_intervals.out" />
-    </test>
-  </tests> -->
-  <help>
-
-.. class:: warningmark
-
-This tool currently only works with data from genome builds hg16, hg17 or hg18.
-
-.. class:: warningmark
-
-This tool expects 2 input datasets, the first in wiggle format and the second in interval format. 
-
------
-
-.. class:: infomark
-
-**TIP:** Aggregating data may throw exceptions if the data type (e.g., string, integer) in every line of the columns is not appropriate for the computation (e.g., attempting numerical calculations on strings).  If an exception is thrown, computation is stopped and an error message is displayed.
-
------
-
-**Syntax**
-
-This tool returns aggregated data per interval in the form of the average, minimum and maximum of the data points for each given interval.
-
-Note: Datapoints must be in the format returned by the table browser.
-
-.. image:: ../../static/images/dat_points_table_brows_1.png
-
------
-
-**Example**
-
-*Input*
-
-.. image:: ../../static/images/aggregate_history1.png
-
-*Result*
-
-.. image:: ../../static/images/aggregate_history2.png
-
-    </help>
-</tool>
diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml
index d69ba6652a6..cdb90aa91c4 100644
--- a/tools/stats/cor.xml
+++ b/tools/stats/cor.xml
@@ -2,7 +2,7 @@
   <description>for numeric columns</description>
   <command interpreter="python">cor.py $input1 $out_file1 $numeric_columns $method</command>
   <inputs>
-    <param format="tabular" name="input1" type="data" label="Dataset" refresh_on_change="True" help="Query missing? See TIP below"/>
+    <param format="tabular" name="input1" type="data" label="Dataset" help="Query missing? See TIP below"/>
     <param name="numeric_columns" label="Numerical columns" type="columnlist" numerical="True" multiple="True" assoc_dataset="input1" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
     <param name="method" type="select" label="Method">
       <option value="pearson">Pearson</option>
diff --git a/tools/stats/grouping.xml b/tools/stats/grouping.xml
index 9fb3599f78d..d3969585631 100644
--- a/tools/stats/grouping.xml
+++ b/tools/stats/grouping.xml
@@ -11,7 +11,7 @@
       #end for
   </command>
   <inputs>
-    <param format="tabular" name="input1" type="data" label="Select data" refresh_on_change="True" help="Query missing? See TIP below."/>
+    <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
     <param name="groupcol" label="Group by column" type="columnlist" assoc_dataset="input1" />
     <repeat name="operations" title="Operation">
       <param name="optype" type="select" label="Type">