diff tool-data/rRNA_databases.loc.sample @ 1:b482293b2987 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 844d980a7de5f199487ca9591420a23df63c5246-dirty

--- a/tool-data/rRNA_databases.loc.sample	Mon Aug 03 08:18:26 2015 -0400
+++ b/tool-data/rRNA_databases.loc.sample	Wed Aug 05 02:50:43 2015 -0400
@@ -1,26 +1,30 @@
 #This is a sample file distributed with Galaxy that is used to define a
-#list of public ribosomal databases, using three columns tab separated
-#(longer whitespace are TAB characters):
+#list of public ribosomal databases for SortMeRNA, using the following format
+#(white space characters are TAB characters):
 #
-#<unique_id>    <database_caption>      <base_name_path>
+#<unique_id>	<database_caption>	<fasta_file_path>
 #
-#It is important that the actual database name does not have a space in it,
-#and that the first tab that appears in the line is right before the 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:
 #
-#So, for example, if your database is rfam-5.8s and the path to your base name
-#is /data/rRNA_databases/rfam-5.8s, 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
 #
-#rfam-5.8s          Rfam 5.8S eukarya            /data/rRNA_databases/rfam-5.8s
+#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:
 #
-#Since SortMeRNA comes bundled with eight ribosomal databases, which are ready
-#for use after the tool installation, this sample file is in fact an actual file
-#to save the user the trouble of setting it.
+#  indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98
 #
-rfam-5.8s	Rfam 5.8S eukarya	$SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta
-rfam-5s	Rfam 5S archaea/bacteria	$SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta
-silva-arc-16s	SILVA 16S archaea	$SORTMERNADIR/rRNA_databases/silva-arc-16s-database-id95.fasta
-silva-arc-23s	SILVA 16S bacteria	$SORTMERNADIR/rRNA_databases/silva-arc-23s-database-id98.fasta
-silva-bac-16s	SILVA 16S bacteria	$SORTMERNADIR/rRNA_databases/silva-bac-16s-database-id85.fasta
-silva-bac-23s	SILVA 23S bacteria	$SORTMERNADIR/rRNA_databases/silva-bac-23s-database-id98.fasta
-silva-euk-18s	SILVA 18S eukarya	$SORTMERNADIR/rRNA_databases/silva-euk-18s-database-id95.fasta
-silva-euk-28s	SILVA 28S eukarya	$SORTMERNADIR/rRNA_databases/silva-euk-28s-database-id98.fasta
+#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 23S archaea	$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