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annotate tool-data/frogs_picrust2_functions.loc.sample @ 25:dfaf556d2a20 draft

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
author oinizan
date Wed, 07 Jun 2023 09:00:18 +0000
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25
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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5 # the Free Software Foundation, either version 3 of the License, or
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6 # (at your option) any later version.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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7 #
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8 # This program is distributed in the hope that it will be useful,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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11 # GNU General Public License for more details.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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12 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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13 # You should have received a copy of the GNU General Public License
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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15 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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16 #
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17 #This is a sample file that enables tools FROGS_frogsfunc_copynumbers to predict
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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18 #the copy number of gene families present in the predicted genome for OTU,
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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19 # given a tree and a set of known trait values (FROGS_frogsfunc_placeseqs).
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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20 #
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21 #PICRUSt2 files are present in the arborescence of PICRUSt2.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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22 #
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23 #<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function>
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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24 #
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25 # For 16S data (see the 6 first lines), PICRUSt2 only takes the dname of the database as input (for exemple EC).
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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26 # With ITS and 18S data, you have to specify the path of marker gene counts files.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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30 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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31 # The indicated path is the one if you do not change the default galaxy config of conda directory.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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32 # Just adapt path by replacing <Galaxy_dir> with the real path and eventually the picrust version.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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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.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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35 #
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36 #
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37 #
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38 #16S EC EC EC
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39 #16S KO KO KO
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40 #16S PFAM PFAM PFAM
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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41 #16S COG COG COG
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42 #16S TIGRFAM TIGRFAM TIGRFAM
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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43 #16S PHENO PHENO PHENO
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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