--- a/tool_data_table_conf.xml.sample	Tue Aug 14 11:14:52 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Aug 14 11:19:49 2018 -0400
@@ -1,5 +1,12 @@
-<?xml version="1.0"?>
 <tables>
-	<table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_gff.loc" /> </table>
-	<table name="representative_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/representative_gff.loc" /> </table>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the kallisto mapper format -->
+    <table name="salmon_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/salmon_indexes.loc" />
+    </table>
 </tables>