diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml
index b9492252710..e42839567fb 100644
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -28,7 +28,7 @@
         tophat2
         
         ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
+        --num-threads \${GALAXY_SLOTS:-4}
 
         ## Set params.
         #if $params.settingsType == "full":
diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml
index 399d2c9c46c..8698fddc6e9 100644
--- a/tools/ngs_rna/tophat_color_wrapper.xml
+++ b/tools/ngs_rna/tophat_color_wrapper.xml
@@ -6,7 +6,7 @@
     <command interpreter="python">
         tophat_wrapper.py
             ## Change this to accommodate the number of threads you have available.
-            --num-threads="4"
+            --num-threads="\${GALAXY_SLOTS:-4}"
 
             ## base- or color-space
             --color-space
diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index a8961fe98a4..ef4bab1fc66 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -10,8 +10,7 @@
     <command interpreter="python">
         tophat_wrapper.py
             ## Change this to accommodate the number of threads you have available.
-            --num-threads="4"
-
+            --num-threads="\${GALAXY_SLOTS:-4}"
             ## Provide outputs.
             --junctions-output=$junctions
             --hits-output=$accepted_hits