diff --git a/test-data/taxonomyGI.txt b/test-data/taxonomyGI.tabular
similarity index 100%
rename from test-data/taxonomyGI.txt
rename to test-data/taxonomyGI.tabular
diff --git a/tools/taxonomy/example_dataset_missing_nodes.txt b/tools/taxonomy/example_dataset_missing_nodes.txt
deleted file mode 100644
index 3e55049f68d..00000000000
--- a/tools/taxonomy/example_dataset_missing_nodes.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-Species_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
-Species_2 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 n species2 subspecies2
-Species_3 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
-Species_4 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
-Species_5 5 root superkingdom1 kingdom1 subkingdom1 superphylum1 n subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species5 subspecies5
-
diff --git a/tools/taxonomy/find_diag_hits.xml b/tools/taxonomy/find_diag_hits.xml
index fd0da7edce2..e57cde42360 100644
--- a/tools/taxonomy/find_diag_hits.xml
+++ b/tools/taxonomy/find_diag_hits.xml
@@ -37,11 +37,11 @@
     </outputs>
       <tests>
     <test>
-      <param name="input1" value="taxonomyGI.dat" ftype="taxonomy"/>
+      <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
       <param name="id_col" value="1" />
       <param name="rank_list" value="order,genus" />
       <param name="out_format" value="counts" />
-      <output name="out_file1" file="find_diag_hits.dat" ftype="tabular"/>
+      <output name="out_file1" file="find_diag_hits.tabular" />
     </test> 
   </tests>
 
diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml
index 35cdbc6c469..5aa68d755fa 100644
--- a/tools/taxonomy/gi2taxonomy.xml
+++ b/tools/taxonomy/gi2taxonomy.xml
@@ -14,10 +14,10 @@
   </requirements>
   <tests>
     <test>
-      <param name="input" value="taxonomy2gi-input.txt"/>
+      <param name="input" ftype="tabular" value="taxonomy2gi-input.tabular"/>
       <param name="giField" value="1"/>
       <param name="idField" value="2"/>
-      <output name="out_file1" file="taxonomy2gi-output.txt"/>
+      <output name="out_file1" file="taxonomy2gi-output.tabular"/>
     </test>
   </tests>
 
diff --git a/tools/taxonomy/poisson2test.xml b/tools/taxonomy/poisson2test.xml
index 57d2b0791a1..a13f97185b4 100644
--- a/tools/taxonomy/poisson2test.xml
+++ b/tools/taxonomy/poisson2test.xml
@@ -16,20 +16,20 @@
   </outputs> 
   <tests>
     <test>
-        <param name="input1" value="poisson2test1.txt"/>
+        <param name="input1" value="poisson2test1.tabular" ftype="tabular"/>
         <param name="input2" value="2" />
         <param name="input3" value="3" />
         <param name="input4" value="0.44" />
         <param name="input5" value="0" />
-        <output name="output1" file="poisson2test1.out" />    
+        <output name="output1" file="poisson2test1_out.tabular" />    
     </test>
     <test>
-        <param name="input1" value="poisson2test2.txt"/>
+        <param name="input1" value="poisson2test2.tabular" ftype="tabular"/>
         <param name="input2" value="2" />
         <param name="input3" value="3" />
         <param name="input4" value="0.44" />
         <param name="input5" value="0" />
-        <output name="output1" file="poisson2test2.out" />    
+        <output name="output1" file="poisson2test2_out.tabular" />    
     </test>    
   </tests>
   <help>
diff --git a/tools/taxonomy/t2t_report.xml b/tools/taxonomy/t2t_report.xml
index 2f953fa98bf..bfaa35aceb6 100644
--- a/tools/taxonomy/t2t_report.xml
+++ b/tools/taxonomy/t2t_report.xml
@@ -12,8 +12,8 @@
   </requirements>
   <tests>
     <test>
-      <param name="input" value="taxonomyGI.dat" ftype="taxonomy"/>
-      <output name="out_file1" file="t2t_report.dat"/>
+      <param name="input" value="taxonomyGI.taxonomy" ftype="taxonomy"/>
+      <output name="out_file1" file="t2t_report.tabular"/>
     </test>
   </tests>