diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 3b18735b5d7..34b9aed2bf5 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -81,7 +81,7 @@
     <tool file="maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml"/>
     <tool file="maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml"/>
     <tool file="maf/maf_limit_size1/1.0.0/maf_limit_size.xml"/>
-    <tool file="maf/maf_by_block_number.xml"/>
+    <tool file="maf/maf_by_block_number1/1.0.0/maf_by_block_number.xml"/>
     <!--    
     <tool file="maf/MAF_Reverse_Complement_1/1.0.0/maf_reverse_complement.xml"/>
     <tool file="maf/MAF_filter/1.0.0/maf_filter.xml"/> 
@@ -110,9 +110,9 @@
     <tool file="stats/cor.xml" /> 
   </section>
   <section name="Graph/Display Data" id="plots">
-    <tool file="plotting/histogram2.xml" />
-    <tool file="plotting/scatterplot.xml" />
-    <tool file="plotting/xy_plot.xml" />
+    <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
+    <tool file="plotting/scatterplot_rpy/1.0.0/scatterplot.xml" />
+    <tool file="plotting/XY_Plot_1/1.0.0/xy_plot.xml" />
     <tool file="visualization/GMAJ.xml" />
     <tool file="visualization/build_ucsc_custom_track.xml" />
   </section>
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 63bcdd43143..fcd43705679 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -87,7 +87,7 @@
     <tool file="maf/MAF_Thread_For_Species1/1.0.0/maf_thread_for_species.xml"/>
     <tool file="maf/MAF_Limit_To_Species1/1.0.0/maf_limit_to_species.xml"/>
     <tool file="maf/maf_limit_size1/1.0.0/maf_limit_size.xml"/>
-    <tool file="maf/maf_by_block_number.xml"/>
+    <tool file="maf/maf_by_block_number1/1.0.0/maf_by_block_number.xml"/>
     <tool file="maf/MAF_Reverse_Complement_1/1.0.0/maf_reverse_complement.xml"/>
     <tool file="maf/MAF_filter/1.0.0/maf_filter.xml"/>
   </section>
@@ -114,9 +114,9 @@
     <tool file="stats/cor.xml" /> 
   </section>
   <section name="Graph/Display Data" id="plots">
-    <tool file="plotting/histogram2.xml" />
-    <tool file="plotting/scatterplot.xml" />
-    <tool file="plotting/xy_plot.xml" />
+    <tool file="plotting/histogram_rpy/1.0.0/histogram2.xml" />
+    <tool file="plotting/scatterplot_rpy/1.0.0/scatterplot.xml" />
+    <tool file="plotting/XY_Plot_1/1.0.0/xy_plot.xml" />
     <tool file="visualization/GMAJ.xml" />
     <tool file="visualization/LAJ.xml" />
     <tool file="visualization/build_ucsc_custom_track.xml" />
diff --git a/tools/plotting/r_wrapper.sh b/tools/plotting/XY_Plot_1/1.0.0/r_wrapper.sh
similarity index 100%
rename from tools/plotting/r_wrapper.sh
rename to tools/plotting/XY_Plot_1/1.0.0/r_wrapper.sh
diff --git a/tools/plotting/xy_plot.xml b/tools/plotting/XY_Plot_1/1.0.0/xy_plot.xml
similarity index 100%
rename from tools/plotting/xy_plot.xml
rename to tools/plotting/XY_Plot_1/1.0.0/xy_plot.xml
diff --git a/tools/plotting/histogram.py b/tools/plotting/histogram_rpy/1.0.0/histogram.py
similarity index 100%
rename from tools/plotting/histogram.py
rename to tools/plotting/histogram_rpy/1.0.0/histogram.py
diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram_rpy/1.0.0/histogram2.xml
similarity index 100%
rename from tools/plotting/histogram2.xml
rename to tools/plotting/histogram_rpy/1.0.0/histogram2.xml
diff --git a/tools/plotting/scatterplot.py b/tools/plotting/scatterplot_rpy/1.0.0/scatterplot.py
similarity index 100%
rename from tools/plotting/scatterplot.py
rename to tools/plotting/scatterplot_rpy/1.0.0/scatterplot.py
diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot_rpy/1.0.0/scatterplot.xml
similarity index 100%
rename from tools/plotting/scatterplot.xml
rename to tools/plotting/scatterplot_rpy/1.0.0/scatterplot.xml