view test-data/databases/frogs_picrust2_functions.loc @ 30:fce825ec2c84 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty

# Copyright (C) 2022 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_frogsfunc_copynumbers to predict 
#the copy number of gene families present in the predicted genome for OTU, 
# given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs).
#
#PICRUSt2 files are present in the arborescence of PICRUSt2. 
#
#<value_as_marker_gene>	<name_as_fun_db>	<fun_db_or_path_to_marker_copy_numbers>	<fun_db_or_path_to_fun_copy_numbers>	<version>

# For 16S data (see the 6 first lines), PICRUSt2 only takes the db name of the database as input (for exemple EC).
# With ITS and 18S data, you have to specify the path of marker gene counts files.
#
#
# Bellow you will find out how to implement this loc file.
#
# The indicated path is the one if you do not change the default galaxy config of conda directory.
# Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version.
#
# If you are not using this default conda behavior, please consult PICRUSt2 documentation to find out where they are located in your environment.
#
#
#
# EXAMPLE FOR TEST :
16S	EC	EC	EC	2.5.1
16S	KO	KO	KO	2.5.1
16S	PFAM	PFAM	PFAM	2.5.1
16S	COG	COG	COG	2.5.1
16S	TIGRFAM	TIGRFAM	TIGRFAM	2.5.1
16S	PHENO	PHENO	PHENO	2.5.1
ITS	EC	${__HERE__}/frogs_picrust2_db/prokaryotic/16S_test.txt.gz	${__HERE__}/frogs_picrust2_db/prokaryotic/ec_test.txt.gz	2.5.1