--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rRNA_databases.loc.sample	Tue Aug 04 15:14:58 2015 -0400
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that is used to define a
+#list of public ribosomal databases for SortMeRNA, using the following format
+#(white space characters are TAB characters):
+#
+#<unique_id>	<database_caption>	<fasta_file_path>
+#
+#So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA
+#file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc
+#entry would look like this:
+#
+#rfam-5.8s-id98	Rfam 5.8S eukarya	/data/rRNA_databases/rfam-5.8s-id98.fasta
+#
+#For each rRNA database, you need to create the index files using the
+#indexdb_rna program provided by SortMeRNA. You need to specify as index
+#basename the path of the FASTA file without extension. For example, for the
+#previous database the command is:
+#
+#  indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98
+#
+#Since SortMeRNA comes bundled with eight ribosomal databases, you can use them
+#by creating the actual index files as explained above and uncommenting the
+#following lines.
+#rfam-5.8s-id98	Rfam 5.8S eukarya	$SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta
+#rfam-5s-id98	Rfam 5S archaea/bacteria	$SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta
+#silva-arc-16s-id95	SILVA v.119 16S archaea	$SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta
+#silva-arc-23s-id98	SILVA v.119 16S bacteria	$SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta
+#silva-bac-16s-id90	SILVA v.119 16S bacteria	$SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta
+#silva-bac-23s-id98	SILVA v.119 23S bacteria	$SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta
+#silva-euk-18s-id95	SILVA v.119 18S eukarya	$SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta
+#silva-euk-28s-id98	SILVA v.119 28S eukarya	$SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta