Mercurial > repos > oinizan > frogs
diff tool-data/frogs_picrust2_pathways.loc.sample @ 25:dfaf556d2a20 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
| author | oinizan |
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| date | Wed, 07 Jun 2023 09:00:18 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_picrust2_pathways.loc.sample Wed Jun 07 09:00:18 2023 +0000 @@ -0,0 +1,37 @@ +# 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_pathways to map pathways to reactions. +#The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways. +# +#PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult +#PICRUSt2 documentation to find out where they are located in your environment. +# +#If you are not comfortable with picrust2 command lines, just create .loc files +#with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path. +# +#The indicated path is the one if you do not change the default galaxy config of conda directory. +# +#<db_id> <db_name> <marker_gene> <path_to_mapfiles> <picrust_version> +# +# +# +# +# EXAMPLE FOR TEST : +#pro_metacyc_pathway Metacyc 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_pro.txt 2.5.1 +#fungi_metacyc_pathway Metacyc ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt 2.5.1 +#fungi_metacyc_pathway Metacyc 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi.txt 2.5.1 +#kegg_modules_pathway Kegg 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/pathway_mapfiles/KEGG_pathways_to_KO.tsv 2.5.1 \ No newline at end of file