diff --git a/test/functional/test_3D_Edit_Modify.py b/test/functional/test_3D_Edit_Modify.py
index 37494a4756e..a93a99046af 100644
--- a/test/functional/test_3D_Edit_Modify.py
+++ b/test/functional/test_3D_Edit_Modify.py
@@ -17,35 +17,35 @@ class EditModifyTests(TwillTestCase):
 
     def test_11_Add_column_1(self):
         """3D_Edit_Modify: Add value 1 to cds"""
-        self.run_tool("addValue", exp="1", iterate="no")
+        self.run_tool("addValue", input=1, exp="1", iterate="no")
         self.wait()
         self.check_data('sc_3D_cds_add_1.bed', hid=2)
 
     def test_12_Add_column_Mycds(self):
         """3D_Edit_Modify: Add value 'My.cds' to cds"""
         self.delete_data(2)
-        self.run_tool("addValue", exp="My.cds", iterate="no")
+        self.run_tool("addValue", input=1, exp="My.cds", iterate="no")
         self.wait()
         self.check_data('sc_3D_cds_add_mycds.bed', hid=3)
 
     def test_21_compute1(self):
         """3D_Edit_Modify: Compute expression c3-c2"""
         self.delete_data(3)
-        self.run_tool('Add a column1', cond='c3-c2')
+        self.run_tool('Add a column1', input=1, cond='c3-c2')
         self.wait()
         self.check_data('sc_3D_cds_compute1.bed', hid=4)
 
     def test_22_compute2(self):
         """3D_Edit_Modify: Compute expression(c3-c2)*100"""
         self.delete_data(4)
-        self.run_tool('Add a column1', cond='(c3-c2)*100')
+        self.run_tool('Add a column1', input=1, cond='(c3-c2)*100')
         self.wait()
         self.check_data('sc_3D_cds_compute2.bed', hid=5)
 
     def test_30_concatenate(self):
         """3D_Edit_Modify: Concatenate cd and cds"""
         self.delete_data(5)
-        self.run_tool('cat1')
+        self.run_tool('cat1', input1=1, input2=1)
         self.wait()
         self.check_data('sc_3D_cds_concat.bed', hid=6)
 
@@ -59,14 +59,14 @@ class EditModifyTests(TwillTestCase):
     def test_50_cut(self):
         """3D_Edit_Modify: cut c1, c2"""
         self.delete_data(7)
-        self.run_tool('Cut1', columnList='c1,c2', delimiter='T')
+        self.run_tool('Cut1', input=1, columnList='c1,c2', delimiter='T')
         self.wait()
         self.check_data('sc_3D_cds_cut.bed', hid=8)
 
     def test_60_paste(self):
         """3D_Edit_Modify: paste"""
         self.delete_data(8)
-        self.run_tool('Paste1', delimiter='T')
+        self.run_tool('Paste1', input1=1, input2=1, delimiter='T')
         self.wait()
         self.check_data('sc_3D_cds_paste.bed', hid=9)
         self.delete_data(9)
diff --git a/test/functional/test_3E_Filter.py b/test/functional/test_3E_Filter.py
index 8a23740a263..2cb8fcf887a 100644
--- a/test/functional/test_3E_Filter.py
+++ b/test/functional/test_3E_Filter.py
@@ -9,8 +9,6 @@ class FilterTests(TwillTestCase):
 
     def test_10_Genes(self):
         """3E_Filter: Get UCSC known genes first(encode)"""
-        self.clear_history()
-
         self.run_tool('ucsc_proxy')
         params = dict(
             hgta_regionType="encode",
@@ -30,14 +28,14 @@ class FilterTests(TwillTestCase):
     def test_21_Sort1(self):
         """3E_Filter: Sort on column one"""
         self.delete_data(2)
-        self.run_tool("sort1", column="1", order="ASC", style="alpha")
+        self.run_tool("sort1", input=1, column="1", order="ASC", style="alpha")
         self.wait()
         self.check_data('sc_3E_sort.bed', hid=3)
 
     def test_31_select(self):
         """3E_Filter: Select on the pattern AY143171"""
         self.delete_data(3)
-        self.run_tool("Grep1", invert="false", pattern="AY143171")
+        self.run_tool("Grep1", input=1, invert="false", pattern="AY143171")
         self.wait()
         self.check_data('sc_3E_select.bed', hid=4)