Mercurial > repos > frogs > frogs_func
diff tool-data/frogs_picrust2_placeseqs.loc.sample @ 0:c5fd7b97c2a4 draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
| author | frogs |
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| date | Wed, 04 Feb 2026 13:17:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/frogs_picrust2_placeseqs.loc.sample Wed Feb 04 13:17:34 2026 +0000 @@ -0,0 +1,42 @@ +# 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_placeseqs to place +#studies sequences (i.e. OTUs) into a reference tree. +# +#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. +# +#<identifier> <marker_gene> <path_to_picrust_dir> <path_to_marker_copy_numbers> <placement_tool> <picrust_version> +# +#default dir must contain these files: +# +# XX.fna +# XX.hmm +# XX.model +# XX.tre +# XX.raxml_info # optional +# +# EXAMPLE FOR TEST : +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/16S_counts.txt.gz epa-ng 2.5.1 +#picrust2_default_dir_16S 16S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/16S_counts.txt.gz sepp 2.5.1 +#picrust2_default_dir_ITS ITS <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_ITS/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz epa-ng 2.5.1 +#picrust2_default_dir_18S 18S <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/fungi_18S/ <Galaxy_dir>/database/dependencies/_conda/envs/<PICRUSt2_env>/lib/python3.6/site-packages/picrust2/default_files/fungi/18S_counts.txt.gz epa-ng 2.5.1