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annotate test-data/databases/frogs_picrust2_functions.loc @ 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
oinizan
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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
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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
oinizan
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5 # the Free Software Foundation, either version 3 of the License, or
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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
oinizan
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7 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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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
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
oinizan
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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
oinizan
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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
oinizan
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15 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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16 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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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. Please consult
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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22 #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
oinizan
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23 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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24 #If you are not comfortable with picrust2 command lines, just create .loc files
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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25 #with EXAMPLE FOR TEST files remembering to replace <PATH_TO> with the real path.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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26 #
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27 #<marker_gene> <db> <picrust2_input_marker> <picrust2_input_function> <picrust_version>
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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28 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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29 #With 16S data, 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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30 #With ITS and 18S data, you have to specify the path of marke gene counts files.
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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31 #
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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32 # EXAMPLE FOR TEST :
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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33 16S EC EC EC 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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34 16S KO KO KO 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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35 16S PFAM PFAM PFAM 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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36 16S COG COG COG 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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37 16S TIGRFAM TIGRFAM TIGRFAM 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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38 16S PHENO PHENO PHENO 2.5.1
dfaf556d2a20 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 281ada90f8ce8630844ca000aa676ed55901661b-dirty
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39 ITS EC ${__HERE__}/frogs_picrust2_db/prokaryotic/16S_test.txt.gz ${__HERE__}/frogs_picrust2_db/prokaryotic/ec_test.txt.gz 2.5.1