diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 81825999f3b..bb1ffc04602 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -25,7 +25,7 @@
   </section>
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/addValue/1.0.0/fixedValueColumn.xml" />
-    <tool file="stats/column_maker.xml" />
+    <tool file="stats/Add_a_column1/1.0.0/column_maker.xml" />
     <tool file="filters/cat1/1.0.0/catWrapper.xml" />
     <tool file="filters/Condense_characters1/1.0.0/condense_characters.xml" />
     <tool file="filters/Convert_characters1/1.0.0/convert_characters.xml" />
@@ -37,7 +37,7 @@
     <tool file="filters/Show_tail1/1.0.0/tailWrapper.xml" />
   </section>
   <section name="Filter and Sort" id="filter">
-    <tool file="stats/filtering.xml" />
+    <tool file="stats/Filter1/1.0.0/filtering.xml" />
     <tool file="filters/sort1/1.0.0/sorter.xml" />
     <tool file="filters/Grep1/1.0.0/grep.xml" />
   </section>
@@ -45,7 +45,7 @@
     <tool file="filters/join1/2.0.0/joiner.xml" />
     <tool file="filters/comp1/1.0.0/compare.xml"/>
     <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
-    <tool file="stats/grouping.xml" />   
+    <tool file="stats/Grouping1/1.0.0/grouping.xml" />   
   </section>
   <section name="Convert Formats" id="convert">
     <tool file="filters/bed2gff1/2.0.0/bed2gff.xml" />
@@ -88,8 +88,8 @@
     -->
   </section>
   <section name="Get Genomic Scores" id="scores">
-    <tool file="stats/wiggle_to_simple.xml" />
-    <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
+    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" />
+    <tool file="stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml" />
     <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
@@ -105,9 +105,9 @@
     <tool file="new_operations/get_flanks1/1.0.0/get_flanks.xml" />
   </section>
   <section name="Statistics" id="stats">
-    <tool file="stats/gsummary.xml" />
+    <tool file="stats/Summary_Statistics1/1.0.0/gsummary.xml" />
     <tool file="filters/Count1/1.0.0/uniq.xml" /> 
-    <tool file="stats/cor.xml" /> 
+    <tool file="stats/cor2/1.0.0/cor.xml" /> 
   </section>
   <section name="Graph/Display Data" id="plots">
     <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 47535277292..9d100d33d3e 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -29,7 +29,7 @@
   </section>
   <section name="Text Manipulation" id="textutil">
     <tool file="filters/addValue/1.0.0/fixedValueColumn.xml" />
-    <tool file="stats/column_maker.xml" />
+    <tool file="stats/Add_a_column1/1.0.0/column_maker.xml" />
     <tool file="filters/cat1/1.0.0/catWrapper.xml" />
     <tool file="filters/Condense_characters1/1.0.0/condense_characters.xml" />
     <tool file="filters/Convert_characters1/1.0.0/convert_characters.xml" />
@@ -41,7 +41,7 @@
     <tool file="filters/Show_tail1/1.0.0/tailWrapper.xml" />
   </section>
   <section name="Filter and Sort" id="filter">
-    <tool file="stats/filtering.xml" />
+    <tool file="stats/Filter1/1.0.0/filtering.xml" />
     <tool file="filters/sort1/1.0.0/sorter.xml" />
     <tool file="filters/Grep1/1.0.0/grep.xml" />
   </section>
@@ -49,7 +49,7 @@
     <tool file="filters/join1/2.0.0/joiner.xml" />
     <tool file="filters/comp1/1.0.0/compare.xml"/>
     <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
-    <tool file="stats/grouping.xml" />   
+    <tool file="stats/Grouping1/1.0.0/grouping.xml" />   
   </section>
   <section name="Convert Formats" id="convert">
     <tool file="filters/axt_to_concat_fasta/1.0.0/axt_to_concat_fasta.xml" />
@@ -92,8 +92,8 @@
     <tool file="maf/MAF_filter/1.0.0/maf_filter.xml"/>
   </section>
   <section name="Get Genomic Scores" id="scores">
-    <tool file="stats/wiggle_to_simple.xml" />
-    <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
+    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" />
+    <tool file="stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml" />
     <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
@@ -109,9 +109,9 @@
     <tool file="new_operations/get_flanks1/1.0.0/get_flanks.xml" />
   </section>
   <section name="Statistics" id="stats">
-    <tool file="stats/gsummary.xml" />
+    <tool file="stats/Summary_Statistics1/1.0.0/gsummary.xml" />
     <tool file="filters/Count1/1.0.0/uniq.xml" /> 
-    <tool file="stats/cor.xml" /> 
+    <tool file="stats/cor2/1.0.0/cor.xml" /> 
   </section>
   <section name="Graph/Display Data" id="plots">
     <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
diff --git a/tools/stats/column_maker.py b/tools/stats/Add_a_column1/1.0.0/column_maker.py
similarity index 100%
rename from tools/stats/column_maker.py
rename to tools/stats/Add_a_column1/1.0.0/column_maker.py
diff --git a/tools/stats/column_maker.xml b/tools/stats/Add_a_column1/1.0.0/column_maker.xml
similarity index 100%
rename from tools/stats/column_maker.xml
rename to tools/stats/Add_a_column1/1.0.0/column_maker.xml
diff --git a/tools/stats/filtering.py b/tools/stats/Filter1/1.0.0/filtering.py
similarity index 100%
rename from tools/stats/filtering.py
rename to tools/stats/Filter1/1.0.0/filtering.py
diff --git a/tools/stats/filtering.xml b/tools/stats/Filter1/1.0.0/filtering.xml
similarity index 100%
rename from tools/stats/filtering.xml
rename to tools/stats/Filter1/1.0.0/filtering.xml
diff --git a/tools/stats/grouping.py b/tools/stats/Grouping1/1.0.0/grouping.py
similarity index 100%
rename from tools/stats/grouping.py
rename to tools/stats/Grouping1/1.0.0/grouping.py
diff --git a/tools/stats/grouping.xml b/tools/stats/Grouping1/1.0.0/grouping.xml
similarity index 100%
rename from tools/stats/grouping.xml
rename to tools/stats/Grouping1/1.0.0/grouping.xml
diff --git a/tools/stats/correlation.pl b/tools/stats/Pearson_and_apos_Correlation1/1.0.0/correlation.pl
similarity index 100%
rename from tools/stats/correlation.pl
rename to tools/stats/Pearson_and_apos_Correlation1/1.0.0/correlation.pl
diff --git a/tools/stats/correlation.xml b/tools/stats/Pearson_and_apos_Correlation1/1.0.0/correlation.xml
similarity index 87%
rename from tools/stats/correlation.xml
rename to tools/stats/Pearson_and_apos_Correlation1/1.0.0/correlation.xml
index ad6e1ba4c31..b82530200de 100644
--- a/tools/stats/correlation.xml
+++ b/tools/stats/Pearson_and_apos_Correlation1/1.0.0/correlation.xml
@@ -1,4 +1,4 @@
-<tool id="Pearson&apos;s Correlation1" name="Pearson&apos;s Correlation">
+<tool id="Pearson_and_apos_Correlation1" name="Pearson and apos Correlation">
   <description>between any two numeric columns</description>
   <command interpreter="perl">correlation.pl $input $out_file1 $col1 $col2</command>
   <inputs>
diff --git a/tools/stats/gsummary.py b/tools/stats/Summary_Statistics1/1.0.0/gsummary.py
similarity index 100%
rename from tools/stats/gsummary.py
rename to tools/stats/Summary_Statistics1/1.0.0/gsummary.py
diff --git a/tools/stats/gsummary.xml b/tools/stats/Summary_Statistics1/1.0.0/gsummary.xml
similarity index 100%
rename from tools/stats/gsummary.xml
rename to tools/stats/Summary_Statistics1/1.0.0/gsummary.xml
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml.old b/tools/stats/aggregate_scores_in_intervals2/1.0.0/aggregate_binned_scores_in_intervals.xml
similarity index 100%
rename from tools/stats/aggregate_binned_scores_in_intervals.xml.old
rename to tools/stats/aggregate_scores_in_intervals2/1.0.0/aggregate_binned_scores_in_intervals.xml
diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml
similarity index 100%
rename from tools/stats/aggregate_binned_scores_in_intervals.xml
rename to tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml
diff --git a/tools/stats/aggregate_scores_in_intervals.py b/tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_scores_in_intervals.py
similarity index 100%
rename from tools/stats/aggregate_scores_in_intervals.py
rename to tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_scores_in_intervals.py
diff --git a/tools/stats/cor.py b/tools/stats/cor2/1.0.0/cor.py
similarity index 100%
rename from tools/stats/cor.py
rename to tools/stats/cor2/1.0.0/cor.py
diff --git a/tools/stats/cor.xml b/tools/stats/cor2/1.0.0/cor.xml
similarity index 100%
rename from tools/stats/cor.xml
rename to tools/stats/cor2/1.0.0/cor.xml
diff --git a/tools/stats/wiggle_to_simple.py b/tools/stats/wiggle2simple1/1.0.0/wiggle_to_simple.py
similarity index 100%
rename from tools/stats/wiggle_to_simple.py
rename to tools/stats/wiggle2simple1/1.0.0/wiggle_to_simple.py
diff --git a/tools/stats/wiggle_to_simple.xml b/tools/stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml
similarity index 100%
rename from tools/stats/wiggle_to_simple.xml
rename to tools/stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml