diff --git a/tools/data_source/encode_import_code.py b/tools/data_source/encode_import_code.py
index 09a6e8a9823..6a706b5ab04 100644
--- a/tools/data_source/encode_import_code.py
+++ b/tools/data_source/encode_import_code.py
@@ -5,7 +5,8 @@ from shutil import copyfile
 
 #post processing, set build for data and add additional data to history
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    history = out_data.items()[0][1].history
+    base_dataset = out_data.items()[0][1]
+    history = base_dataset.history
     if history == None:
         print "unknown history!"
         return
@@ -37,6 +38,8 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.extension = file_type
             newdata.name = basic_name + " (" + description + ")"
             history.add_dataset( newdata )
+            app.security_agent.set_dataset_groups( newdata.dataset, base_dataset.dataset.groups )
+            app.security_agent.set_dataset_roles( newdata.dataset, base_dataset.dataset.roles )
             app.model.flush()
             try:
                 copyfile(filepath,newdata.file_name)
diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py
index b6bc2f6bd85..ad6a877e353 100644
--- a/tools/data_source/microbial_import_code.py
+++ b/tools/data_source/microbial_import_code.py
@@ -84,7 +84,8 @@ from galaxy import datatypes, config, jobs
 from shutil import copyfile
 
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
-    history = out_data.items()[0][1].history
+    base_dataset = out_data.items()[0][1]
+    history = base_dataset.history
     if history == None:
         print "unknown history!"
         return
@@ -128,6 +129,8 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             newdata.extension = file_type
             newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")"
             newdata.flush()
+            app.security_agent.set_dataset_groups( newdata.dataset, base_dataset.dataset.groups )
+            app.security_agent.set_dataset_roles( newdata.dataset, base_dataset.dataset.roles )
             history.add_dataset( newdata )
             app.model.flush()
             try:
diff --git a/tools/maf/maf_to_bed_code.py b/tools/maf/maf_to_bed_code.py
index c8f1e905e8e..d3784661188 100644
--- a/tools/maf/maf_to_bed_code.py
+++ b/tools/maf/maf_to_bed_code.py
@@ -27,12 +27,13 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
             fields = line.split("\t")
             dbkey = fields[1]
             filepath = fields[2]
-
             newdata = app.model.HistoryDatasetAssociation( create_dataset = True )
             newdata.extension = "bed"
             newdata.name = basic_name + " (" + dbkey + ")"
             newdata.flush()
             history.add_dataset( newdata )
+            app.security_agent.set_dataset_groups( newdata.dataset, output_data.dataset.groups )
+            app.security_agent.set_dataset_roles( newdata.dataset, output_data.dataset.roles )
             newdata.flush()
             history.flush()
             app.model.flush()