view tool-data/frogs_picrust2_functions.loc.sample @ 0:c5fd7b97c2a4 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

# 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>	<PICRUSt2_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.
#
#
#
#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	<Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz	<Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz	2.5.1
#18S	EC	<Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz	<Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ec_18S_counts.txt.gz	2.5.1