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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
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1 # Copyright (C) 2022 INRA
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2 #
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3 # This program is free software: you can redistribute it and/or modify
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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
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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
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6 # (at your option) any later version.
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7 #
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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
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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
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11 # GNU General Public License for more details.
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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/>.
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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_copynumbers to predict
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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18 #the copy number of gene families present in the predicted genome for OTU,
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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19 # given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs).
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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20 #
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21 #PICRUSt2 files are present in the arborescence of PICRUSt2.
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22 #
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23 #<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>
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24
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25 # For 16S data (see the 6 first lines), PICRUSt2 only takes the db name of the database as input (for exemple EC).
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26 # With ITS and 18S data, you have to specify the path of marker gene counts files.
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27 #
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28 #
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29 # Bellow you will find out how to implement this loc file.
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30 #
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31 # The indicated path is the one if you do not change the default galaxy config of conda directory.
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32 # Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version.
7275d6a514d2 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0e048f8e3dfce3c6abe2facd83ab95d62d42dab8
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33 #
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34 # If you are not using this default conda behavior, please consult PICRUSt2 documentation to find out where they are located in your environment.
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35 #
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36 #
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37 #
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38 #16S EC EC EC 2.5.1
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39 #16S KO KO KO 2.5.1
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40 #16S PFAM PFAM PFAM 2.5.1
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41 #16S COG COG COG 2.5.1
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42 #16S TIGRFAM TIGRFAM TIGRFAM 2.5.1
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43 #16S PHENO PHENO PHENO 2.5.1
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44 #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
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45 #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