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# Copyright (C) 2014 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#This is a sample file that enables tools FROGS_affiliations_OTU to use taxonomy database for
#taxonomy affiliation. You will need to create or download Blast+ index and train your database
#for RDP classifier these data files.
#download link : http://genoweb.toulouse.inra.fr/frogs_databanks/assignation
#Finally you will need to create frogs_db.loc file similar to this one in your galaxy
#tool-data directory.The frogs_db.loc file has this format (longer white space characters are
#TAB characters):
#
#<unique_database_name>   <file_path>
#
#First column will be the visible name in galaxy.
#So, for example, if you had 16S silva 128 indexed stored in
#/galaxy_databanks/16S/silva_128/ 
#then the frogs_db.loc entry would look like this:
#
#silva 128 16S  /galaxy_databanks/16S/silva_128/silva_128_16S.fasta
#
#and your /galaxy_databanks/16S/silva_128/ directory
#would contain index files:
#
#-rw-r--r-- 1 mbernard FROGS    8097966  5 déc.  16:56 bergeyTrainingTree.xml
#-rw-r--r-- 1 mbernard FROGS 1572981589  5 déc.  16:56 genus_wordConditionalProbList.txt
#-rw-r--r-- 1 mbernard FROGS       1654  5 déc.  16:56 LICENCE.txt
#-rw-r--r-- 1 mbernard FROGS    1072228  5 déc.  16:56 logWordPrior.txt
#-rw-r--r-- 1 mbernard FROGS  940834335  5 déc.  16:56 silva_128_16S.fasta
#-rw-r--r-- 1 mbernard FROGS  152606489  5 déc.  16:56 silva_128_16S.fasta.nhr
#-rw-r--r-- 1 mbernard FROGS    6918588  5 déc.  16:56 silva_128_16S.fasta.nin
#-rw-r--r-- 1 mbernard FROGS  205320030  5 déc.  16:56 silva_128_16S.fasta.nsq
#-rw-r--r-- 1 mbernard FROGS        281  5 déc.  16:56 silva_128_16S.fasta.properties
#-rw-r--r-- 1 mbernard FROGS    3420464  5 déc.  16:56 silva_128_16S.tax
#-rw-r--r-- 1 mbernard FROGS     964048  5 déc.  16:57 wordConditionalProbIndexArr.txt
#
#
#<name>    <name>    <file_path>
#
# EXAMPLE FOR TEST :
#ITS1_test	ITS1_test	${__HERE__}/frogs_db_data/ITS1.rdp.fasta