Mercurial > repos > oinizan > frogs_func

annotate tool-data/frogs_picrust2_pathways.loc.sample @ 0:7275d6a514d2 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
author oinizan
date Wed, 28 Jan 2026 16:20:19 +0000
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7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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1 # Copyright (C) 2022 INRA
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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2 #
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3 # This program is free software: you can redistribute it and/or modify
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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4 # it under the terms of the GNU General Public License as published by
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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5 # the Free Software Foundation, either version 3 of the License, or
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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6 # (at your option) any later version.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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7 #
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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8 # This program is distributed in the hope that it will be useful,
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
oinizan
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11 # GNU General Public License for more details.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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12 #
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13 # You should have received a copy of the GNU General Public License
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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15 #
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16 #
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17 #This is a sample file that enables tools FROGS_frogsfunc_pathways to map pathways to reactions.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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18 #The default mapfile maps MetaCyc reactions to prokaryotic MetaCyc pathways.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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19 #
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20 #PICRUSt2 files are present in the arborescence of PICRUSt2. Please consult
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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21 #PICRUSt2 documentation to find out where they are located in your environment.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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22 #
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23 #If you are not comfortable with picrust2 command lines, just create .loc files
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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24 #with EXAMPLE FOR TEST files remembering to replace <Galaxy_dir> with the real path.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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25 #
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26 #The indicated path is the one if you do not change the default galaxy config of conda directory.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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27 #
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28 #<db_id> <db_name> <marker_gene> <path_to_mapfiles> <picrust_version>
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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29 #
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30 #
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31 #
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32 #
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33 # EXAMPLE FOR TEST :
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34 #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
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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35 #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
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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36 #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
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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37 #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