--- a/tool-data/fasta_indexes.loc.sample	Wed Dec 04 16:21:13 2013 -0500
+++ b/tool-data/fasta_indexes.loc.sample	Thu Jan 09 14:27:59 2014 -0500
@@ -1,8 +1,8 @@
 #This is a sample file distributed with Galaxy that enables tools
 #to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_new_indices.loc file
+#to create these data files and then create a fasta_indexes.loc file
 #similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The sam_fa_new_indices.loc
+#the directories in which those files are stored. The fasta_indexes.loc
 #file has this format (white space characters are TAB characters):
 #
 # <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
@@ -11,14 +11,14 @@
 #
 # /depot/data2/galaxy/hg19/sam/,
 #
-#then the sam_fa_new_indices.loc entry would look like this:
+#then the fasta_indexes.loc entry would look like this:
 #
 #hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
 #
 #and your /depot/data2/galaxy/hg19/sam/ directory
 #would contain hg19canon.fa and hg19canon.fa.fai files.
 #
-#Your sam_fa_new_indices.loc file should include an entry per line for
+#Your fasta_indexes.loc file should include an entry per line for
 #each index set you have stored.  The file in the path does actually
 #exist, but it should never be directly used. Instead, the name serves
 #as a prefix for the index file.  For example: