diff --git a/tools/phenotype_association/dividePgSnpAlleles.xml b/tools/phenotype_association/dividePgSnpAlleles.xml
index df8485551d1..874d47521ae 100644
--- a/tools/phenotype_association/dividePgSnpAlleles.xml
+++ b/tools/phenotype_association/dividePgSnpAlleles.xml
@@ -25,7 +25,7 @@
   <tests>
     <test>
       <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' />
-      <param name='refcol' value='no' />
+      <param name='ref' value='no' />
       <output name="output" file="dividePgSnp_output.txt" />
     </test>
   </tests>
diff --git a/tools/phenotype_association/snpFreq.xml b/tools/phenotype_association/snpFreq.xml
index 100ab471b6d..12d9dce5c02 100644
--- a/tools/phenotype_association/snpFreq.xml
+++ b/tools/phenotype_association/snpFreq.xml
@@ -44,6 +44,7 @@
 
   <tests>
     <test>
+      <param name="inType" value="tab" />
       <param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" />
       <param name="group1_1" value="4" />
       <param name="group1_2" value="5" />